CODEWITHSUNDEEP
rbioinformatics
Thiago Vidotto
Thiago Vidotto

Reputation: 33

Saving .maf file as a table

I am trying to save a .maf file as a table, but I always get the error below:

Error in as.data.frame.default(x[[i]], optional = TRUE) : 
  cannot coerce class ‘structure("MAF", package = "maftools")’ to a data.frame

This is the code I am using:

library(maftools)

laml.maf <- "/Users/PC/mc3.v0.2.8.PUBLIC.maf"
laml = read.maf(maf = laml.maf)

write.table(laml, file="/Users/PC/tp53atm.txt")

I understand that the .maf file has several fields, but I am not sure how to isolate them to save as a table. Any help would be much appreciated!

Upvotes: 3

Views: 1813

Answers (1)

mrhd
mrhd

Reputation: 1076

The problem is, that the write.table function doesn't know how to deal with an object of class MAF.

However, you can access the underlying data like this:

write.table(laml@data, file="/Users/PC/tp53atm.txt")

But note that this way you will only export the raw data, whereas the MAF object contains various other meta data:

> slotNames(laml)
[1] "data"                           "variants.per.sample"            "variant.type.summary"           "variant.classification.summary"
[5] "gene.summary"                   "summary"                       
 "maf.silent"                     "clinical.data"                 
>

Upvotes: 4

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