diff --git a/vignettes/get_projects.R b/vignettes/get_projects.R
new file mode 100644
index 0000000..d2cf7f4
--- /dev/null
+++ b/vignettes/get_projects.R
@@ -0,0 +1,39 @@
+library(GenomicDataCommons)
+
+
+#more than one possibility to get availble projects on the gdc portal
+#perhaps useful for anyone searching for gdc data to combine with existing laboratory samples
+gdc_proj<-projects()
+
+#get available keys to build queries
+#available_fields(gdc_proj)
+#facet(gdc_proj)
+
+####get available gdc projects
+res_1<-(gdc_proj |> facet('project_id') |> aggregations() )
+#save to file
+write.csv(res$project_id$key,file="project_id.txt",quote=FALSE,row.names=FALSE)
+
+#get gdc project names
+res_2<-(gdc_proj |> facet('program.name') |> aggregations() )
+#Save to file
+write.csv(res$program.name$key,file=='program.name.txt',quote=FALSE,row.names=FALSE)
+
+#addtional exp details
+res_3<-(gdc_proj |> facet('name') |> aggregations() )
+#get list components
+#names(res)
+write.csv(res$name["key"],file=='project_name.txt',quote=FALSE,row.names=FALSE)
+
+#get biospecimen, tissue site 
+res_4<-(gdc_proj |> facet('primary_site') |> aggregations() )
+
+write.csv(res$primary_site['key'],file=='primary_site.txt',quote=FALSE,row.names=FALSE)
+
+####use multiple fields
+res_5<-(gdc_proj |> facet(gdc_proj$fields[c(4:5,7)]) |> aggregations() )
+
+x<-list(N=res$name["key"],P=res$project_id["key"],T=res$primary_site["key"])
+
+#save to file , not a 1-1 map
+#cat(capture.output(print(x), file="test.txt"))
diff --git a/vignettes/mmrf_commpass_wgs.R b/vignettes/mmrf_commpass_wgs.R
new file mode 100644
index 0000000..8624de2
--- /dev/null
+++ b/vignettes/mmrf_commpass_wgs.R
@@ -0,0 +1,34 @@
+
+
+#building queries
+
+#get  available info for project MMRF-COMMPASS
+q_1 = files() |> GenomicDataCommons::filter(cases.project.project_id == 'MMRF-COMMPASS') |> manifest()
+
+#save info to file for future use
+write.csv(q_1,file="out.txt",quote=FALE,row.names=FALSE)
+
+#list only open access entries
+q_2 = files() |> GenomicDataCommons::filter(cases.project.project_id == 'MMRF-COMMPASS') |> filter(access == "open")|> manifest()
+
+# restrict data to WGS  
+
+
+q_3=files() |> GenomicDataCommons::filter(cases.project.project_id == 'MMRF-COMMPASS') |> filter(access == "open") |> filter(experimental_strategy == "WGS") |> manifest() 
+
+
+#restrict data to WGS Copy Number Segment
+q_4=files() |> GenomicDataCommons::filter(cases.project.project_id == 'MMRF-COMMPASS') |> filter(access == "open") |> filter(experimental_strategy == "WGS" & data_type == 'Copy Number Segment') |> manifest() 
+
+
+#get files less than size 32000
+
+q_5=files() |> GenomicDataCommons::filter(cases.project.project_id == 'MMRF-COMMPASS') |> filter(access == "open") |> filter(experimental_strategy == "WGS" & data_type == 'Copy Number Segment' & file_size < 32000) |> manifest() 
+
+#get the files
+for(i in seq(1,dim(q_5)[1]))
+{
+uid<-0;
+uid<-as.character(q_6[i,"id"])
+gdcdata(uid)
+}
diff --git a/vignettes/mmrf_commpass_wxs.R b/vignettes/mmrf_commpass_wxs.R
new file mode 100644
index 0000000..b04e128
--- /dev/null
+++ b/vignettes/mmrf_commpass_wxs.R
@@ -0,0 +1,34 @@
+
+
+#building queries
+
+#get  available info for project MMRF-COMMPASS
+q_1 = files() |> GenomicDataCommons::filter(cases.project.project_id == 'MMRF-COMMPASS') |> manifest()
+
+#save info to file for future use
+write.csv(q_3,file="out.txt",quote=FALE,row.names=FALSE)
+
+#list only open access entries
+q_2 = files() |> GenomicDataCommons::filter(cases.project.project_id == 'MMRF-COMMPASS') |> filter(access == "open")|> manifest()
+
+# restrict data to WXS  
+
+
+q_3=files() |> GenomicDataCommons::filter(cases.project.project_id == 'MMRF-COMMPASS') |> filter(access == "open") |> filter(experimental_strategy == "WXS") |> manifest() 
+
+
+#restrict data to WXS Masked Somatic Mutation
+q_4=files() |> GenomicDataCommons::filter(cases.project.project_id == 'MMRF-COMMPASS') |> filter(access == "open") |> filter(experimental_strategy == "WXS" & data_type == 'Masked Somatic Mutation') |> manifest() 
+
+
+#list files by timestamp
+
+q_5=files() |> GenomicDataCommons::filter(cases.project.project_id == 'MMRF-COMMPASS') |> filter(access == "open") |> filter(experimental_strategy == "WXS" & data_type == 'Masked Somatic Mutation' & created_datetime < "2022-08-22T10:48:06.705961-05:00" ) |> manifest() 
+
+#get the files
+for(i in seq(1,dim(q_5)[1]))
+{
+uid<-0;
+uid<-as.character(q_5[i,"id"])
+gdcdata(uid)
+}
diff --git a/vignettes/overview.Rmd b/vignettes/overview.Rmd
index 17a1114..4269cda 100644
--- a/vignettes/overview.Rmd
+++ b/vignettes/overview.Rmd
@@ -118,6 +118,12 @@ stopifnot(GenomicDataCommons::status()$status=="OK")
 
 
 ## Find data
+Please use a fresh R session to minimise package conflicts arising from identical function names.
+For example the functions filter(), results() are available with R packages dplyr, GenomicDataCommons . Instead consider using the R package conflicted.
+Example usage
+conflicts_prefer(dplyr::filter())
+conflicts_prefer(GenomicDataCommons::filter)
+conflicts_prefer(stats :: filter)
 
 The following code builds a `manifest` that can be used to guide the
 download of raw data. Here, filtering finds gene expression files
@@ -164,8 +170,8 @@ the `gdc_clinical()` function will return a list of four `tibble`s.
 - main
 
 ```{r gdc_clinical}
-case_ids = cases() |> results(size=10) |> ids()
-clindat = gdc_clinical(case_ids)
+case_ids <- cases() |> results(size=10) |> ids()
+clindat <- gdc_clinical(case_ids)
 names(clindat)
 ```
 
@@ -183,9 +189,9 @@ be all that is needed, but the API and `r Biocpkg("GenomicDataCommons")` package
 make much flexibility if fine-tuning is required. 
 
 ```{r metadataQS}
-expands = c("diagnoses","annotations",
+expands <- c("diagnoses","annotations",
              "demographic","exposures")
-clinResults = cases() |>
+clinResults <- cases() |>
     GenomicDataCommons::select(NULL) |>
     GenomicDataCommons::expand(expands) |>
     results(size=50)
@@ -287,7 +293,7 @@ functions that each create `GDCQuery` objects (actually, specific subclasses of
 - `annotations()`
 
 ```{r projectquery}
-pquery = projects()
+pquery <- projects()
 ```
 
 The `pquery` object is now an object of (S3) class, `GDCQuery` (and
@@ -326,16 +332,16 @@ Note that we have not set any filters, so a `count()` here will represent all
 the project records publicly available at the GDC in the "default" archive"
 
 ```{r pquerycount}
-pcount = count(pquery)
+pcount <- count(pquery)
 # or
-pcount = pquery |> count()
+pcount <- pquery |> count()
 pcount
 ```
 
 The `results()` method will fetch actual results.
 
 ```{r pqueryresults}
-presults = pquery |> results()
+presults <- pquery |> results()
 ```
 These results are
 returned from the GDC in [JSON](http://www.json.org/) format and
@@ -356,7 +362,7 @@ size is probably warranted before calling `results_all()`
 
 ```{r presultsall}
 length(ids(presults))
-presults = pquery |> results_all()
+presults <- pquery |> results_all()
 length(ids(presults))
 # includes all records
 length(ids(presults)) == count(pquery)
@@ -401,11 +407,11 @@ the dplyr `select()` verb that limits from already-present fields. We
 
 ```{r selectexample}
 # Default fields here
-qcases = cases()
+qcases <- cases()
 qcases$fields
 # set up query to use ALL available fields
 # Note that checking of fields is done by select()
-qcases = cases() |> GenomicDataCommons::select(available_fields('cases'))
+qcases <- cases() |> GenomicDataCommons::select(available_fields('cases'))
 head(qcases$fields)
 ```
 
@@ -428,7 +434,7 @@ tibbles).
 
 ```{r aggexample}
 # total number of files of a specific type
-res = files() |> facet(c('type','data_type')) |> aggregations()
+res <- files() |> facet(c('type','data_type')) |> aggregations()
 res$type
 ```
 
@@ -454,7 +460,7 @@ For the user, these details will not be too important except to note that a
 filter expression must begin with a "~".
 
 ```{r allfilesunfiltered}
-qfiles = files()
+qfiles <- files()
 qfiles |> count() # all files
 ```
 To limit the file type, we can refer back to the
@@ -463,7 +469,7 @@ the file field "type". For example, to filter file results to only
 "gene_expression" files, we simply specify a filter.
 
 ```{r onlyGeneExpression}
-qfiles = files() |> filter( type == 'gene_expression')
+qfiles <- files() |> filter( type == 'gene_expression')
 # here is what the filter looks like after translation
 str(get_filter(qfiles))
 ```
@@ -495,7 +501,7 @@ note that `TCGA-OV` is the correct project_id, not `TCGA-OVCA`. Note that
 filter and does not build on any previous filters*.
 
 ```{r filtfinal}
-qfiles = files() |>
+qfiles <- files() |>
     filter( cases.project.project_id == 'TCGA-OV' & type == 'gene_expression')
 str(get_filter(qfiles))
 qfiles |> count()
@@ -507,7 +513,7 @@ accomplish the same effect as multiple `&` conditionals. The `count()`
 below is equivalent to the `&` filtering done above.
 
 ```{r filtChain}
-qfiles2 = files() |>
+qfiles2 <- files() |>
     filter( cases.project.project_id == 'TCGA-OV') |> 
     filter( type == 'gene_expression') 
 qfiles2 |> count()
@@ -520,7 +526,7 @@ Generating a manifest for bulk downloads is as
 simple as asking for the manifest from the current query.
 
 ```{r filtAndManifest}
-manifest_df = qfiles |> manifest()
+manifest_df <- qfiles |> manifest()
 head(manifest_df)
 ```
 
@@ -531,11 +537,11 @@ that the field "analysis.workflow_type" has the appropriate filter criteria.
 
 
 ```{r filterForSTARCounts}
-qfiles = files() |> filter( ~ cases.project.project_id == 'TCGA-OV' &
+qfiles <- files() |> filter( ~ cases.project.project_id == 'TCGA-OV' &
                             type == 'gene_expression' &
                             access == "open" &
                             analysis.workflow_type == 'STAR - Counts')
-manifest_df = qfiles |> manifest()
+manifest_df <- qfiles |> manifest()
 nrow(manifest_df)
 ```
 
@@ -577,7 +583,7 @@ be stored in one of three ways (resolved in this order):
 As a concrete example:
 
 ```{r authenNoRun, eval=FALSE}
-token = gdc_token()
+token <- gdc_token()
 transfer(...,token=token)
 # or
 transfer(...,token=get_token())
@@ -594,7 +600,7 @@ ids. A simple way of producing such a vector is to produce a
 contain file ids.
 
 ```{r singlefileDL}
-fnames = gdcdata(manifest_df$id[1:2],progress=FALSE)
+fnames <- gdcdata(manifest_df$id[1:2],progress=FALSE)
 
 ```
 
@@ -614,7 +620,7 @@ in parallel.
 ```{r bulkDL, eval=FALSE}
 # Requires gcd_client command-line utility to be isntalled
 # separately. 
-fnames = gdcdata(manifest_df$id[3:10], access_method = 'client')
+fnames <- gdcdata(manifest_df$id[3:10], access_method = 'client')
 ```
 
 
@@ -627,7 +633,7 @@ fnames = gdcdata(manifest_df$id[3:10], access_method = 'client')
 ### How many cases are there per project_id?
 
 ```{r casesPerProject}
-res = cases() |> facet("project.project_id") |> aggregations()
+res <- cases() |> facet("project.project_id") |> aggregations()
 head(res)
 library(ggplot2)
 ggplot(res$project.project_id,aes(x = key, y = doc_count)) +
@@ -653,7 +659,7 @@ cases() |> filter(~ project.program.name=='TCGA') |> count()
 # The need to do the "&" here is a requirement of the
 # current version of the GDC API. I have filed a feature
 # request to remove this requirement.
-resp = cases() |> filter(~ project.project_id=='TCGA-BRCA' &
+resp <- cases() |> filter(~ project.project_id=='TCGA-BRCA' &
                               project.project_id=='TCGA-BRCA' ) |>
     facet('samples.sample_type') |> aggregations()
 resp$samples.sample_type
@@ -665,12 +671,12 @@ resp$samples.sample_type
 # The need to do the "&" here is a requirement of the
 # current version of the GDC API. I have filed a feature
 # request to remove this requirement.
-resp = cases() |> filter(~ project.project_id=='TCGA-BRCA' &
+resp <- cases() |> filter(~ project.project_id=='TCGA-BRCA' &
                               samples.sample_type=='Solid Tissue Normal') |>
     GenomicDataCommons::select(c(default_fields(cases()),'samples.sample_type')) |>
     response_all()
 count(resp)
-res = resp |> results()
+res <- resp |> results()
 str(res[1],list.len=6)
 head(ids(resp))
 ```
@@ -721,7 +727,7 @@ cases() |>
 ### How many of each type of file are available?
 
 ```{r filesVCFCount}
-res = files() |> facet('type') |> aggregations()
+res <- files() |> facet('type') |> aggregations()
 res$type
 ggplot(res$type,aes(x = key,y = doc_count)) + geom_bar(stat='identity') +
     theme(axis.text.x = element_text(angle = 45, hjust = 1))
@@ -730,13 +736,13 @@ ggplot(res$type,aes(x = key,y = doc_count)) + geom_bar(stat='identity') +
 ### Find gene-level RNA-seq quantification files for GBM
 
 ```{r filesRNAseqGeneGBM}
-q = files() |>
+q <- files() |>
     GenomicDataCommons::select(available_fields('files')) |>
     filter(~ cases.project.project_id=='TCGA-GBM' &
                data_type=='Gene Expression Quantification')
 q |> facet('analysis.workflow_type') |> aggregations()
 # so need to add another filter
-file_ids = q |> filter(~ cases.project.project_id=='TCGA-GBM' &
+file_ids <- q |> filter(~ cases.project.project_id=='TCGA-GBM' &
                             data_type=='Gene Expression Quantification' &
                             analysis.workflow_type == 'STAR - Counts') |>
     GenomicDataCommons::select('file_id') |>
@@ -752,20 +758,20 @@ file_ids = q |> filter(~ cases.project.project_id=='TCGA-GBM' &
 and for vignette building**.
 
 ```{r filesRNAseqGeneGBMforBAM}
-q = files() |>
+q <- files() |>
     GenomicDataCommons::select(available_fields('files')) |>
     filter(~ cases.project.project_id == 'TCGA-GBM' &
                data_type == 'Aligned Reads' &
                experimental_strategy == 'RNA-Seq' &
                data_format == 'BAM')
-file_ids = q |> response_all() |> ids()
+file_ids <- q |> response_all() |> ids()
 ```
 
 
 ```{r slicing10, eval=FALSE}
-bamfile = slicing(file_ids[1],regions="chr12:6534405-6538375",token=gdc_token())
+bamfile <- slicing(file_ids[1],regions="chr12:6534405-6538375",token=gdc_token())
 library(GenomicAlignments)
-aligns = readGAlignments(bamfile)
+aligns <- readGAlignments(bamfile)
 ```
 
 # Troubleshooting
diff --git a/vignettes/questions-and-answers.Rmd b/vignettes/questions-and-answers.Rmd
index 67fcf74..d8649d6 100644
--- a/vignettes/questions-and-answers.Rmd
+++ b/vignettes/questions-and-answers.Rmd
@@ -29,7 +29,7 @@ changes to lazy evaluation best practices. There is now no need to
 include the `~` in the filter expression. So:
 
 ```{r}
-q = files() |>
+q <- files() |>
   GenomicDataCommons::filter(
     cases.project.project_id == 'TCGA-COAD' &
       data_type == 'Aligned Reads' &
@@ -51,7 +51,7 @@ manifest(q)
 Your question about race and ethnicity is a good one. 
 
 ```{r}
-all_fields = available_fields(files())
+all_fields <- available_fields(files())
 ```
 
 And we can grep for `race` or `ethnic` to get potential matching fields
@@ -72,7 +72,7 @@ available_values('files',"cases.demographic.race")
 We can complete our filter expression now to limit to `white` race only.
 
 ```{r}
-q_white_only = q |>
+q_white_only <- q |>
   GenomicDataCommons::filter(cases.demographic.race=='white')
 count(q_white_only)
 manifest(q_white_only)
diff --git a/vignettes/somatic_mutations.Rmd b/vignettes/somatic_mutations.Rmd
index 4268c16..1c6c975 100644
--- a/vignettes/somatic_mutations.Rmd
+++ b/vignettes/somatic_mutations.Rmd
@@ -38,7 +38,7 @@ head(available_values('genes','symbol'))
 
 
 ```{r}
-tp53 = genes() |> 
+tp53 <- genes() |> 
   GenomicDataCommons::filter(symbol=='TP53') |> 
   results(size=10000) |> 
   as_tibble()
@@ -67,7 +67,7 @@ ssms() |>
 
 ```{r warning=FALSE,message=FALSE}
 library(VariantAnnotation)
-vars = ssms() |> 
+vars <- ssms() |> 
     GenomicDataCommons::filter(
       consequence.transcript.gene.symbol %in% c('TP53')) |> 
     GenomicDataCommons::results_all() |>
@@ -75,7 +75,7 @@ vars = ssms() |>
 ```
 
 ```{r}
-vr = VRanges(seqnames = vars$chromosome,
+vr <- VRanges(seqnames = vars$chromosome,
              ranges = IRanges(start=vars$start_position, width=1),
              ref = vars$reference_allele,
              alt = vars$tumor_allele)
@@ -89,7 +89,7 @@ ssm_occurrences() |>
 ```
 
 ```{r}
-var_samples = ssm_occurrences() |> 
+var_samples <- ssm_occurrences() |> 
     GenomicDataCommons::filter(
       ssm.consequence.transcript.gene.symbol %in% c('TP53')) |> 
     GenomicDataCommons::expand(c('case', 'ssm', 'case.project')) |>
@@ -119,7 +119,7 @@ fnames <- files() |>
 
 ```{r cache=TRUE}
 library(maftools)
-melanoma = read.maf(maf = fnames)
+melanoma <- read.maf(maf = fnames)
 ```
 
 ```{r}
diff --git a/vignettes/ssm_examples.R b/vignettes/ssm_examples.R
new file mode 100644
index 0000000..0d6f225
--- /dev/null
+++ b/vignettes/ssm_examples.R
@@ -0,0 +1,51 @@
+library(dplyr)
+library(tibble)
+library(GenomicDataCommons)
+
+#build queries to get simple somatic mutations
+q_primsite_1 = ssm_occurrences() |> GenomicDataCommons::filter(case.primary_site== 'Esophagus') |> GenomicDataCommons::expand(c('ssm','case')) |> GenomicDataCommons::results_all() |> as_tibble()
+
+#add search criteria
+q_primsite_2 = ssm_occurrences() |> GenomicDataCommons::filter(case.primary_site== 'Esophagus' & case.lost_to_followup == 'No' ) |> GenomicDataCommons::expand(c('ssm','case')) |> GenomicDataCommons::results_all() |> as_tibble()
+
+################
+q_consent = ssm_occurrences() |> GenomicDataCommons::filter(case.consent_type== 'Consent by Death') |> GenomicDataCommons::expand(c('ssm','case')) |> GenomicDataCommons::results_all() |> as_tibble()
+
+write.csv(q_consent,file="ssm_consentbyDeath.txt",row.names=FALSE,quote=FALSE)
+
+q_del = ssm_occurrences() |> GenomicDataCommons::filter(ssm.mutation_subtype == 'Small deletion') |> GenomicDataCommons::expand(c('ssm')) |> GenomicDataCommons::results_all() |> as_tibble()
+
+write.csv(q_del,file="ssm_subtypeDeletions.txt",row.names=FALSE,quote=FALSE)
+
+#get simple somatic mutations on chr one
+q_chrone = ssm_occurrences() |> GenomicDataCommons::filter(ssm.chromosome == 'chr1') |> GenomicDataCommons::expand(c('ssm')) |> GenomicDataCommons::results_all() |> as_tibble()
+
+write.csv(q_chrone,file="simplesomaticmutschr1.txt",row.names=FALSE,quote=FALSE)
+
+######################------------------------------################################
+####get all simple somatic mutations on chr 17
+q_1 = ssm_occurrences() |> GenomicDataCommons::filter(ssm.chromosome == 'chr17') |> GenomicDataCommons::expand(c('ssm')) |> GenomicDataCommons::results_all() |> as_tibble()
+
+write.csv(q_1,file="simplesomaticmutschr17.txt",row.names=FALSE,quote=FALSE)
+
+
+#pull  mutations on chr17 for TP53
+
+q_2 = ssm_occurrences() |> GenomicDataCommons::filter(ssm.consequence.transcript.gene.symbol == 'TP53' & ssm.chromosome == 'chr17') |> GenomicDataCommons::expand(c('case','ssm')) |> GenomicDataCommons::results_all() |> as_tibble()
+
+write.csv(q_2,file="TP53var_samples17.txt",row.names=FALSE,quote=FALSE)
+#sanity check: TP53 gene located on chr17 , so same results
+q_3 = ssm_occurrences() |> GenomicDataCommons::filter(ssm.consequence.transcript.gene.symbol == 'TP53') |> GenomicDataCommons::expand(c('case','ssm')) |> GenomicDataCommons::results_all() |> as_tibble()
+
+write.csv(q_3,file="TP53var_samples.txt",row.names=FALSE,quote=FALSE)
+
+
+#pull  mutations on chr17 for NF1
+q_4 = ssm_occurrences() |> GenomicDataCommons::filter(ssm.consequence.transcript.gene.symbol == 'NF1' & ssm.chromosome == 'chr17') |> GenomicDataCommons::expand(c('case','ssm')) |> GenomicDataCommons::results_all() |> as_tibble()
+
+write.csv(q_4,file="NF1var_samples17.txt",row.names=FALSE,quote=FALSE)
+
+#sanity check : NF1 gene located on chr17, so same results
+q_5 = ssm_occurrences() |> GenomicDataCommons::filter(ssm.consequence.transcript.gene.symbol == 'NF1') |> GenomicDataCommons::expand(c('case','ssm')) |> GenomicDataCommons::results_all() |> as_tibble()
+write.csv(q_5,file="NF1var_samples.txt",row.names=FALSE,quote=FALSE)
+
diff --git a/vignettes/target_cn.R b/vignettes/target_cn.R
new file mode 100644
index 0000000..547a681
--- /dev/null
+++ b/vignettes/target_cn.R
@@ -0,0 +1,21 @@
+library(GenomicDataCommons)
+library(dplyr)
+library(tibble)
+#Clear Cell Sarcoma of the Kidney. Disease Type. Complex Mixed and Stromal Neoplasms. Primary Site. Kidney. Program. TARGET
+
+
+cn_manifest_CCSK <- files() |> GenomicDataCommons::filter( cases.project.project_id == 'TARGET-CCSK') |>  GenomicDataCommons::filter( analysis.workflow_type == 'ASCAT2')  |> manifest()
+n<-which(cn_manifest_CCSK$access=='open')
+
+#save dat to file
+write.csv(cn_manifest_CCSK[n,],file='out.txt',quote=FALSE,row.names=FALSE)
+##########----------#######################
+#select files
+for( i in seq(1,length(n)))
+{
+#
+id<-0;
+        id<-as.character(cn_manifest_CCSK[n[i],1])
+###### 
+gdcdata(id)
+}
diff --git a/vignettes/target_methylation.R b/vignettes/target_methylation.R
new file mode 100644
index 0000000..1f54692
--- /dev/null
+++ b/vignettes/target_methylation.R
@@ -0,0 +1,21 @@
+library(GenomicDataCommons)
+library(dplyr)
+library(tibble)
+#Clear Cell Sarcoma of the Kidney. Disease Type. Complex Mixed and Stromal Neoplasms. Primary Site. Kidney. Program. TARGET
+
+#get familiar with aggregations
+q_2 = files() |> GenomicDataCommons::filter(cases.project.project_id == 'TARGET-CCSK') |> facet(c("data_type","data_format","analysis.workflow_type","file_id","file_name")) |> aggregations()
+
+
+
+q_1 = files() |> GenomicDataCommons::filter(cases.project.project_id == 'TARGET-CCSK') |> facet(c("data_type","data_format","analysis.workflow_type")) |> aggregations()
+
+idat_manifest_CCSK <- files() |> GenomicDataCommons::filter( cases.project.project_id == 'TARGET-CCSK') |> GenomicDataCommons::filter( data_type == 'Methylation Beta Value' ) |> GenomicDataCommons::filter( analysis.workflow_type == 'SeSAMe Methylation Beta Estimation')  |> manifest()
+n<-which(idat_manifest_CCSK$access=='open')
+
+#save data to file
+write.csv(idat_manifest_CCSK[n,],file='manifest.txt',quote=FALSE,row.names=FALSE)
+
+
+###### test  single file 
+gdcdata(idat_manifest_CCSK[n[1],1]))
diff --git a/vignettes/target_methylation_1.R b/vignettes/target_methylation_1.R
new file mode 100644
index 0000000..2c091c4
--- /dev/null
+++ b/vignettes/target_methylation_1.R
@@ -0,0 +1,17 @@
+library(GenomicDataCommons)
+library(dplyr)
+library(tibble)
+
+
+idat_manifest_CCSK <- files() |> GenomicDataCommons::filter( cases.project.project_id == 'TARGET-CCSK') |> GenomicDataCommons::filter( data_type == 'Methylation Beta Value' ) |> GenomicDataCommons::filter( analysis.workflow_type == 'SeSAMe Methylation Beta Estimation')  |> manifest()
+n<-which(idat_manifest_CCSK$access=='open')
+
+##########----------#######################
+for( i in seq(1,length(n)))
+{
+#use cast
+id<-0;
+	id<-as.character(idat_manifest_CCSK[n[i],1])
+######only test with single file 
+gdcdata(id)
+}
diff --git a/vignettes/tcgaTHCA_clinical.R b/vignettes/tcgaTHCA_clinical.R
new file mode 100644
index 0000000..6a34221
--- /dev/null
+++ b/vignettes/tcgaTHCA_clinical.R
@@ -0,0 +1,14 @@
+library(dplyr)
+library(tibble)
+library(GenomicDataCommons)
+
+#get files for project TCGA-THCA
+#build a manifest file 
+#use col names  with function calls
+p_2 = files() |> GenomicDataCommons::filter(cases.project.project_id == 'TCGA-THCA' & data_category == 'Clinical' & data_type == 'Clinical Supplement' & data_format == 'BCR XML')  |> filter(access == "open") |> manifest()
+#get select data
+for(i in seq(20,24))
+{
+uid<-0;uid<-as.character(p_2[i,1])
+gdcdata(uid)
+}
diff --git a/vignettes/tcgaTHCA_pathology.R b/vignettes/tcgaTHCA_pathology.R
new file mode 100644
index 0000000..6288dd9
--- /dev/null
+++ b/vignettes/tcgaTHCA_pathology.R
@@ -0,0 +1,33 @@
+library(dplyr)
+library(tibble)
+library(GenomicDataCommons)
+
+
+# get pathology reports
+q_2 = files() |> GenomicDataCommons::filter(cases.project.project_id == 'TCGA-THCA' & data_category == 'Clinical' & data_type == 'Pathology Report') |> manifest()
+
+for(i in seq(20,24))
+{
+uid<-0;uid<-as.character(q_2[i,1])
+gdcdata(uid)
+}
+
+#use updated datetime to filter data
+q_3 = files() |> GenomicDataCommons::filter(cases.project.project_id == 'TCGA-THCA' & data_category == 'Clinical' & data_type == 'Pathology Report' &  (updated_datetime ==  "2022-12-06T15:32:24.960627-06:00")) |> manifest()
+
+#or 
+
+q_4 = files() |> GenomicDataCommons::filter(cases.project.project_id == 'TCGA-THCA' & data_category == 'Clinical' & data_type == 'Pathology Report' &  (updated_datetime > "2022-12-06T15:32:24.960627-06:00")) |> manifest()
+
+for(i in seq(20,24))
+{
+uid<-0;uid<-as.character(q_4[i,1])
+gdcdata(uid)
+}
+
+#use file size to filter and updated datetime
+#single hit
+q_5 = files() |> GenomicDataCommons::filter(cases.project.project_id == 'TCGA-THCA' & data_category == 'Clinical' & data_type == 'Pathology Report' &  (updated_datetime == "2022-12-06T15:32:24.960627-06:00") & file_size < 2350000) |> manifest()
+#get one file that fits above criteria
+gdcdata(q_5[1,"id"])
+
diff --git a/vignettes/tcga_CEL.R b/vignettes/tcga_CEL.R
new file mode 100644
index 0000000..5cceb52
--- /dev/null
+++ b/vignettes/tcga_CEL.R
@@ -0,0 +1,28 @@
+library(dplyr)
+library(tibble)
+library(GenomicDataCommons)
+
+#
+
+q_2 = files() |> GenomicDataCommons::filter(cases.project.project_id == 'TCGA-GBM' & data_category == 'Transcriptome Profiling' & data_format == 'CEL') |> manifest()
+#OR use filter fn
+q_3 = files() |> GenomicDataCommons::filter(cases.project.project_id == 'TCGA-GBM' & data_category == 'Transcriptome Profiling' & data_format == 'CEL') |> GenomicDataCommons::filter(access=='OPEN') |> manifest()
+
+for(i in seq(10,12))
+{
+uid<-0;
+uid<-as.character(q_3[i,1])
+gdcdata(uid)
+}
+
+
+#
+n<-which(q_2["access"] == 'open')
+for(j in seq(2,3))
+{
+Id<-0
+Id<-as.character(q_3[n[j],1])
+gdcdata(Id)
+}
+
+
diff --git a/vignettes/tcga_proteome.R b/vignettes/tcga_proteome.R
new file mode 100644
index 0000000..d4dd688
--- /dev/null
+++ b/vignettes/tcga_proteome.R
@@ -0,0 +1,29 @@
+library(dplyr)
+library(tibble)
+library(GenomicDataCommons)
+
+p_2 = files() |> GenomicDataCommons::filter(cases.project.project_id == 'TCGA-THCA' & data_type == 'Protein Expression Quantification' & data_format == 'tsv') |> manifest()
+#locate open data
+open_access<-which(p_2$access=="open")
+#381 files
+#download select files 
+#for(i in length(open_access))
+#for(i in seq(3,5))
+#for(i in seq(20,24))
+
+for(i in seq(200,202))
+{
+uid<-0;uid<-as.character(p_2[open_access[i],1])
+gdcdata(uid)
+}
+
+#sanity check , use the filter function 
+
+
+p_3 = files() |> GenomicDataCommons::filter(cases.project.project_id == 'TCGA-THCA' & data_type == 'Protein Expression Quantification' & data_format == 'tsv') |> filter(access == 'open') |> manifest()
+
+for(i in seq(20,24))
+{
+uid<-0;uid<-as.character(p_3[i,1])
+gdcdata(uid)
+}
diff --git a/vignettes/tcga_slides.R b/vignettes/tcga_slides.R
new file mode 100644
index 0000000..f260f3d
--- /dev/null
+++ b/vignettes/tcga_slides.R
@@ -0,0 +1,25 @@
+library(dplyr)
+library(tibble)
+library(GenomicDataCommons)
+
+#specify project name
+#q_2 = files() |> GenomicDataCommons::filter(cases.project.project_id == 'TCGA-KIRC' & data_type == 'Slide Image' & data_format == 'svs') |> manifest()
+q_2 = files() |> GenomicDataCommons::filter(cases.project.project_id == 'TCGA-BRCA' & data_type == 'Slide Image' & data_format == 'svs') |> manifest()
+#locate open data
+open_access<-which(q_2$access=="open")
+
+#select files
+#for(i in length(open_access))
+#for(i in seq(3,5))
+#for(i in seq(20,24))
+for(i in seq(200,202))
+{
+uid<-0;uid<-as.character(q_2[open_access[i],1])
+gdcdata(uid)
+}
+
+
+######alternatively, use filter 
+#both approaches should list same files
+q_3 = files() |> GenomicDataCommons::filter(cases.project.project_id == 'TCGA-BRCA' & data_type == 'Slide Image' & data_format == 'svs') |> filter(access == 'open') |>  manifest()
+
diff --git a/vignettes/tcga_slides_1.R b/vignettes/tcga_slides_1.R
new file mode 100644
index 0000000..057547b
--- /dev/null
+++ b/vignettes/tcga_slides_1.R
@@ -0,0 +1,27 @@
+library(dplyr)
+library(tibble)
+library(GenomicDataCommons)
+
+q_2 = files() |> GenomicDataCommons::filter(cases.project.project_id == 'TCGA-COAD' & data_type == 'Slide Image' & data_format == 'svs') |> manifest()
+#locate open data
+open_access<-which(q_2$access=="open")
+
+#for(i in length(open_access))
+#for(i in seq(3,5))
+#for(i in seq(20,24))
+for(i in seq(200,202))
+{
+uid<-0;uid<-as.character(q_2[open_access[i],1])
+gdcdata(uid)
+}
+
+
+#or sanity check
+
+q_3 = files() |> GenomicDataCommons::filter(cases.project.project_id == 'TCGA-COAD' & data_type == 'Slide Image' & data_format == 'svs') |> filter(access == 'open') |> manifest()
+
+for(i in seq(2,4))
+{
+uid<-0;uid<-as.character(q_3[i,1])
+gdcdata(uid)
+}