Open Pravithaks opened 1 year ago
In the analysis I have mentioned two sample type, solid tissue normal and primary tumor. But in the result file, only primary tumor is present. Please let me know about this. A part of the code below:
query_all = GDCquery(project = c("TCGA-PRAD"), data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantification", experimental.strategy = "RNA-Seq", workflow.type = "STAR - Counts")
barcodes_all = getResults(query_all, cols=c("cases"))
query_normal = GDCquery(project = c("TCGA-PRAD"), data.category = "Transcriptome Profiling", experimental.strategy = "RNA-Seq", workflow.type = "STAR - Counts", sample.type=c("Solid Tissue Normal"))
barcodes_normal = getResults(query_normal, cols=c("cases"))
barcodes_samples = barcodes_all[!(barcodes_all) %in% barcodes_normal]
library(SummarizedExperiment) library(dplyr) library(TCGAbiolinks) query_samples <- GDCquery( project = c("TCGA-PRAD"), data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantification", experimental.strategy = "RNA-Seq", workflow.type = "STAR - Counts", sample.type = "Primary Tumor" ) query_samples$results[[1]] <- query_samples$results[[1]][1:80,] GDCdownload(query_samples) pca <- GDCprepare(query_samples) plyr::count(colData(pca) %>% as.data.frame(),c("ajcc_clinical_m","prior_malignancy")) pca <- pca[,which(pca$prior_malignancy == "no" & pca$ajcc_clinical_m == "M0")]
In the analysis I have mentioned two sample type, solid tissue normal and primary tumor. But in the result file, only primary tumor is present. Please let me know about this.
A part of the code below:
collect all barcodes in the project
query_all = GDCquery(project = c("TCGA-PRAD"), data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantification", experimental.strategy = "RNA-Seq", workflow.type = "STAR - Counts")
barcodes_all = getResults(query_all, cols=c("cases"))
query_normal = GDCquery(project = c("TCGA-PRAD"), data.category = "Transcriptome Profiling", experimental.strategy = "RNA-Seq", workflow.type = "STAR - Counts", sample.type=c("Solid Tissue Normal"))
barcodes_normal = getResults(query_normal, cols=c("cases"))
barcodes_samples = barcodes_all[!(barcodes_all) %in% barcodes_normal]
library(SummarizedExperiment) library(dplyr) library(TCGAbiolinks) query_samples <- GDCquery( project = c("TCGA-PRAD"), data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantification", experimental.strategy = "RNA-Seq", workflow.type = "STAR - Counts", sample.type = "Primary Tumor" ) query_samples$results[[1]] <- query_samples$results[[1]][1:80,] GDCdownload(query_samples) pca <- GDCprepare(query_samples) plyr::count(colData(pca) %>% as.data.frame(),c("ajcc_clinical_m","prior_malignancy")) pca <- pca[,which(pca$prior_malignancy == "no" & pca$ajcc_clinical_m == "M0")]