Reading Clinical data with maftool

Hello,

I want to read my clinical data using maf tools. The data is in tsv format and I am reading it using the code; read.maf(maf = "var.annovar.maf", clinicalData = "clinical_data.tsv", verbose = FALSE))

But i am getting this error Error in is.data.frame(x = maf) : argument "maf" is missing, with no default

What should I do?

Could you try running with read.maf("var.annovar.maf", "clinical_data.tsv") and also posting your session information? @shhabnsbwjd

Hi, What is var.annovar.maf? Is it a file or a data.frame?

Hi, What is var.annovar.maf? Is it a file or a data.frame?

Yes, this is the file I made after converting my annovartomaf

Could you try running with read.maf("var.annovar.maf", "clinical_data.tsv") and also posting your session information? @shhabnsbwjd

Yes sure, let me try

not working

Hi, It says the file does not exist. Please make sure you are providing the correct and full path to the file.

@shhabnsbwjd Try dir(), you may find the file does not exist as @PoisonAlien pointed out. You need to locate your file and set the full path to it, or you need to set working directory to the directory path where your data located with setwd().

This issue is stale because it has been open for 60 days with no activity.

This issue was closed because it has been inactive for 14 days since being marked as stale.