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

Description Usage Arguments Value See Also Examples

View source: R/checkBdev.R

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.

Usage

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checkBdev(object, rsCol = 1, ChrCol = 2, PosCol = 3, LRRCol = 4,
  BAFCol = 5, top = 0.9, bot = 0.1, trim = 0.1, mc.cores,
  quiet = FALSE, hg = "hg18", pval.sig = 0.05, ...)

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.

bot

Inferior treshold to consider an heterozygous allele.

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.

pval.sig

p-value treshold to be used in the classification test.

...

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

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

isglobal-brge/MADloy documentation built on June 11, 2017, 2:40 a.m.