primary tumor-HTSeq count data

Question

[Rob]

Hi all

I downloaded HTSeq file but these are about 600 patients. How can I filter for primary tumors and not all patient?

I tried the following code to exclude non-primary samples but I get error. with this code I could download the data file but when I added line: sample.type = "Primary solid Tumor"I get error

Please help me.

CancerProject <- "TCGA-KIRC"
query <- GDCquery(project = CancerProject,
                  data.category = "Transcriptome Profiling",
                  data.type = "Gene Expression Quantification",
                  sample.type = "Primary solid Tumor"
                  workflow.type = "HTSeq - Counts")

error: Error: unexpected symbol in: " sample.type = "Primary solid Tumor" workflow.type"

[Kevin Blighe]

Please stick to the previous thread: C: TCGAbiolinks HT-Seq count

Answer 1

[Ram]

OP was asked to open a new question there as this is in fact a new question that is related to the previous Q.

@rhasanvandj, you're missing a comma. Use sample.type = "Primary solid tumor", work....

[Rob]

Hi Rams It worked Thanks

[Ram]