Closed selkamand closed 1 year ago
@selkamand Thanks for your suggestion, it is a reasonable request. I will take a look, however, it would take one or two weeks as I am quite busy recently.
@selkamand Could you try installing the latest version from Github? A function read_maf_minimal()
has been added to fit your needs.
An example is given in the doc:
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools", mustWork = TRUE)
if (!require("R.utils")) {
message("Please install 'R.utils' package firstly")
} else {
laml <- read_maf(maf = laml.maf)
laml
laml_mini <- laml@data[, list(
Tumor_Sample_Barcode, Chromosome,
Start_Position, End_Position,
Reference_Allele, Tumor_Seq_Allele2
)]
laml2 <- read_maf_minimal(laml_mini)
laml2
}
For a minimal MAF, you need to provide the following columns:
Tumor_Sample_Barcode, Chromosome, Start_Position, End_Position, Reference_Allele, Tumor_Seq_Allele2
Reference_Allele is Ref, Tumor_Seq_Allele2 is Alt, Tumor_Sample_Barcode is Sample.
Hi @ShixiangWang thanks for a prompt response and update!
I've played around with read_maf_minimal
and it works well
Hi,
Thanks for you work on this amazing package!
Would you consider adding the ability to supply a simple, minimal dataframe as input (e.g. Sample/Chrom/Pos/Ref/Alt)?
This would make it very convenient to run - especially if your pulling data from a non MAF-format database.
The idea being that if the input only requires the data that's absolutely required, to further minimise barriers to entry