HT-Seq count data coding gene

Question

[Rob]

Hi friends I am using R code to download HT-Seq count data Does anybody know what line should I add to the code to download only coding genes? because my code output is all genes (coding& non-coding)

my code:

  CancerProject <- "TCGA-KIRC"
query <- GDCquery(project = CancerProject,
                  data.category = "Transcriptome Profiling",
                  data.type = "Gene Expression Quantification",
                  sample.type = c("Primary Tumor"),
                  workflow.type = "HTSeq - Counts")
#download raw counts for DESEq2
GDCdownload(query)
data <- GDCprepare(query, save = TRUE, save.filename = "exp.rda")
rna <- as.data.frame(SummarizedExperiment::assay(data)) # exp matrix
write.csv(rna, "rna.csv")
clinical <- data.frame(data@colData) # associated clinical data
write.csv(clinical, "clinical.csv")

Answer 1

[Hamid Ghaedi]

To my end, there is no way to do this in data download step, since there is no annotation on what genes are coding for available in TCGA data. You can retrive data on Gene type from BioMart via biomaRt package in a data.frame and then use this to filter your matrix.

This function should retrive needed data from BioMart:

library(biomaRt)

gen.type <-function(ids){
  mart <- useDataset("hsapiens_gene_ensembl", useMart("ensembl"))
  anno <- getBM(filters= "ensembl_gene_id", # if your expression matrix is gene symbol use "hgnc_symbol"
                 attributes= c("ensembl_gene_id","hgnc_symbol", "gene_biotype"),
                 values=ids, mart= mart)
  return(anno)
}

df <- gen.type(row.names(rna)) # this will return a data frame contains Ensembl gene id, gene symbol and gene type.