checkBdev: Check the B deviation values in PAR1 and PAR2 regions to...

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

Check the B deviation values in PAR1 and PAR2 regions to check possible Loss of Y events in a folder or files.

Description

checkBdev checks the B deviation values of all the MAD files specified or in a path to check for possible Loss of Y events. The Bdev is computed by default for the PAR1 and PAR2 regions. The minimum cellularity detected in losses is 26 the detection of false positives.

Usage

checkBdev(
  object,
  rsCol = 1,
  ChrCol = 2,
  PosCol = 3,
  LRRCol = 4,
  BAFCol = 5,
  top = 0.85,
  bot = 0.15,
  trim = 0.1,
  mc.cores,
  quiet = FALSE,
  hg = "GRCh38",
  pval.sig = 0.05,
  bdev.threshold = 0.06,
  ...
)

Arguments

object	A LOY class object to check the LOY and uncertain samples or 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 field.
BAFCol	The position of the column with the BAF field.
top	Superior treshold to consider an heterozygous allele. By default is set to 0.85.
bot	Inferior treshold to consider an heterozygous allele. By default is set to 0.15.
trim	trim the fraction (0 to 0.5) of probes to be trimmed when summaryzing LRR.
mc.cores	The number of cores used to perform the function. By default is set to 1.
quiet	Should the function not inform about the status of the process. By default is FALSE.
hg	Human genome build version. By default set to "GRCh38".
pval.sig	p-value treshold to be used in the classification test. By default is set to 0.05.
bdev.threshold	bdev threshold to determine if there is BAF split significant enough to call an altered region. By default is set to 0.05.
...	Other parameters.

Value

A MADloyBdev object that contains the Bdev values for the two PAR regions for all the files analyzed.

See Also

getLOY to process results from MADloy

Examples

## Not run: 
checkBdev(filepath, mc.cores=2)
## End(Not run)

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