Like as_maftools_obj but for multiple CNAqc objects, it creates
a unique [maftools](https://bioconductor.org/packages/release/bioc/html/maftools.html)
object with all the samples at once.
Parameters have the same meaning as for function as_maftools_obj.
as_maftools_cohort(
x,
only_drivers = TRUE,
CNA_genes = NULL,
clinicalData = NULL,
CNA_map_function = function(cn) {
if (is.na(cn))
return(NA)
A =
strsplit(cn, ":")[[1]][1]
B = strsplit(cn, ":")[[1]][2]
if (A == "NA" |
is.na(A))
return(NA)
if (B == "NA" | is.na(B))
return(NA)
if (cn == "1:1")
return(NA)
if (cn == "1:0")
return("LOH")
if (cn == "2:0")
return("CNLOH")
if (cn == "2:1")
return("Amplification")
if (cn == "2:2")
return("Amplification")
if (B == "0")
return("LOH")
return("Amplification")
}
)A list of CNAqc objects with MAF annotations.
If `TRUE`, only driver mutations are used, otherwised all. When `TRUE`, if drivers are not annotated, an error is thrown.
Gene names (from MAF.Hugo_Symbol) for which we want to report the copy number value.
Clinical data in the format of the maftools package, in the form of a dataframe with a column `"Tumor_Sample_Barcode"` reporting sample names and a column for every clinical annotation to include.
A function that returns, for a copy number value in CNAqc format (e.g., `"1:0"`) a label that is used by the MAF cohort. By default, for instance, `"1:0"` is mapped to `"LOH"`, `"2:0"` to `"CNLOH"`, `"2:1"` and `"2:2"` to `"Amplification"`, and `"1:1"` to `NA`. Use `NA` to avoid reporting the copy number in the MAF cohort.
function augment_with_maf to add MAF annotations to a
CNAqc object, to be used before running `as_maftools_obj`.
if(FALSE)
{
# Create your CNAqc object (omissis here) from an original "file.vcf"
x = init(mutations = ..., cna = ..., purity = ...)
# Offline, create your MAF annotations as file "file_vcf.maf" from "file.vcf"
# vcf2maf file.vcf .... file_vcf.maf
# Import into R/CNAqc
x = augment_with_maf(x, maf = "file_vcf.maf")
# Extraction
x %>% as_maftools_obj
}