Build data for prediction from ASCAT result files

Source: R/buildflow.R

This is is a wrapper of gcap.extractFeatures() and gcap.collapse2Genes() to combine the feature extraction and predict input generate procedure. If you want to modify the result of gcap.extractFeatures(), you should always use the two functions instead of this wrapper.

gcap.runBuildflow(
  ascat_files,
  extra_info,
  include_type = FALSE,
  genome_build = c("hg38", "hg19", "mm10"),
  overlap = 1
)

Arguments

ascat_files

a list of file path. Typically the result of gcap.runASCAT()

extra_info

(optional) a data.frame with 3 columns 'sample', 'age' and 'gender', for including cancer type, check parameter include_type. For gender, should be 'XX' or 'XY', also could be 0 for 'XX' and 1 for 'XY'.

include_type

if TRUE, a fourth column named 'type' should be included in extra_info, the supported cancer type should be described with TCGA cancer type abbr..

genome_build

genome build version, should be one of 'hg38', 'hg19'.

overlap

the overlap percentage on gene.

Value

a data.table.