callAmplificationsInLowPurity {PureCN} | R Documentation |
Function to extract amplification from a
runAbsoluteCN
return object in samples of too low purity
for the standard callAlterations
.
callAmplificationsInLowPurity( res, normalDB, pvalue.cutoff = 0.001, percentile.cutoff = 90, min.width = 3, all.genes = FALSE, purity = NULL, BPPARAM = NULL )
res |
Return object of the |
normalDB |
Normal database, created with
|
pvalue.cutoff |
Copy numbers log-ratio cutoffs to call
amplifications as calculating using the log-ratios observed in
|
percentile.cutoff |
Only report genes with log2-ratio mean exceeding this sample-wise cutoff. |
min.width |
Minimum number of targets |
all.genes |
If |
purity |
If not |
BPPARAM |
|
A data.frame
with gene-level amplification calls.
Markus Riester
data(purecn.example.output) normal.coverage.file <- system.file("extdata", "example_normal.txt", package="PureCN") normal2.coverage.file <- system.file("extdata", "example_normal2.txt", package="PureCN") normal.coverage.files <- c(normal.coverage.file, normal2.coverage.file) normalDB <- createNormalDatabase(normal.coverage.files) callAmplificationsInLowPurity(purecn.example.output, normalDB)["EIF2A", ]