checkSex: Check sex for SNP array samples

In isglobal-brge/MADloy: Package to detect mosaic LOY from SNP array data

Check sex for SNP array samples

Description

Check sex for SNP array samples

Usage

checkSex(
  files,
  rsCol = 1,
  ChrCol = 2,
  PosCol = 3,
  LRRCol = 4,
  mc.cores,
  trim = 0.2,
  quiet = FALSE
)

Arguments

files	A single file path (APT platform and MAD platform), a vector of file paths (MAD platform) or a MAD rawData folder path containing files ready to be processed with MAD (MAD platform).
rsCol	The position of the column with the SNP identifier.
ChrCol	The position of the column with the Chromosome field.
PosCol	The position of the column with the Position field.
LRRCol	The position of the column with the LRR identifier.
mc.cores	The number of cores used to perform the function. By default is set to 1.
trim	the fraction (0 to 0.5) of probes to be trimmed when summaryzing LRR. This argument tries to control the effect of having CNVs across genome. Default is 0.2.
quiet	Should the function not inform about the status of the process. By default is FALSE.

Value

A checkSex object that contains the trimmed mean LRR in chrX and chrY in the analyzed samples, and its classification as males and females in the class variableinside the object.

Examples

## Not run: 
checkSex(filepath, mc.cores=20)
## End(Not run)

isglobal-brge/MADloy documentation built on March 3, 2024, 7:27 p.m.