madloy: Check the mean LRR values in msY region to detect Loss of Y...

Description Usage Arguments Value See Also Examples

Description

madloy check the median log R ratio(LRR) of all the MAD files specified or in a path to detect Loss of Y events. The LRR is computed by default for the autosomes and msY chrY:2694521-59034049 (hg19/GRCh37).

Usage

1
2
3
madloy(files, target.region, ref.region = "Autosomes", rsCol = 1,
  ChrCol = 2, PosCol = 3, LRRCol = 4, trim = 0.05, offset, mc.cores,
  quiet = FALSE, hg = "hg18", ...)

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).

target.region

The chromosome or region to be compared with the other regions. By default is the region chrY:2694521-59034049 (hg19/GRCh37) but it can be changed.

ref.region

If declared, the chromosome or region to be compared with the Y region in UCSC style (i.e. "chr21" or "chr21:1000-10000").

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.

trim

trim the fraction (0 to 0.5) of probes to be trimmed when summaryzing LRR. By default is 0.05.

offset

median value of summarized LRR at target region

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.

...

Other parameters.

Value

A MADloy object that contains the LRR means for all the files analyzed.

See Also

getLOY to process results from MADloy

Examples

1
2
3
## Not run: 
madloy(filepath, mc.cores=2)
## End(Not run)

isglobal-brge/madloy_v1 documentation built on May 6, 2019, 11:46 a.m.