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

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

Check the mean LRR values in msY region to detect Loss of Y events in a folder or files.

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

madloy(
  files,
  target.region,
  ref.region = "Autosomes",
  qc.sds = 0.28,
  rsCol = 1,
  ChrCol = 2,
  PosCol = 3,
  LRRCol = 4,
  trim = 0.05,
  offset,
  mc.cores,
  quiet = FALSE,
  hg = "GRCh38",
  ...
)

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").
qc.sds	Theshold to perform quality control of samples using the reference region/chromosome. The default value is 0.28. It implies that samples having LRR standard deviation larger that this value in the reference chromosome will be removed from the analyses. This value is taken from www.illumina.com/content/dam/illumina-marketing/documents/products/appnotes/appnote_cnv_loh.pdf) If NULL the cutoff for considering a good quality sample is estimated as 2 times the standard deviation of all samples.
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.
hg	Human genome build version. It can be 'hg18', 'hg19' or 'GRCh38'. Set by default to 'GRCh38'.
...	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

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

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