HT-Seq count data coding gene

Question

[Rob]

Hello friends, I want to download HT-seq data from TCGA biolink. How can I download only coding genes? what should I add to my code? this is the code I am using:

library(TCGAbiolinks)
library(SummarizedExperiment)
BiocManager::install("BioinformaticsFMRP/TCGAbiolinks")

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")

[Hamid Ghaedi]

Dear rhasanvandj , As far as I know, there is no code for doing this at the download step. You need to download data and perform your analysis. Then you can select those genes you are interested in (here coding gene).

Having a list of genes you can retrieve data on their Biotype (including coding and non-coding and ...) from Ensembl by biomaRt package.

[Rob]

Thank you so much dear Hamid

Answer 1

[Barry Digby]

This is what Hamid Ghaedi is referring to:

## filter for protein coding genes in matrix (currently > 50,000 rows)
mart <- useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")
mrna_attributes <- getBM(attributes=c("external_gene_name",
                                      "ensembl_gene_id",
                                      "gene_biotype"),
                         filters = c("ensembl_gene_id"),
                         values = rownames(rna),
                         mart = mart)
mrna_attributes <- mrna_attributes[which(mrna_attributes$gene_biotype == "protein_coding"),]
rna <- rna[which(rownames(rna) %in% mrna_attributes$ensembl_gene_id),]

[Rob]

Thanks Barry I tried this code but I got this error:

Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'rownames': object 'rna' not found

[Hamid Ghaedi]

Then make sure you have rna file , it complained that you have not such file. See the very end of error message:

....object 'rna' not found