CheckAbnChr: CheckAbnChr

Description Usage Arguments Details Value Author(s) Source Examples

View source: R/CheckAbnChr.R

Description

CheckAbnChr: Estimate abnormal chromosome.

Usage

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  CheckAbnChr(Path2RawFiles = "/media/NeoScreen/NeSc_home/ILMN/iPSYCH/Version2",
  Cores = 1, Pattern = "*.txt$", skip = 10, NumFiles = "All")

Arguments

Path2RawFiles:

Path for the Log R Ratio (LRR) and B Allele Frequency (BAF) files. Example: "/media/NeoScreen/NeSc_home/ILMN/iPSYCH/Version2".

Cores:

Number of cores to run in parallel, default = 1.

Pattern:

Files pattern in the path. Example: "*.txt$".

Skip:

Integer, the number of lines of the data file to be skipped before beginning to read data. Use if file has comments, default = 10.

NumFiles:

Number of files to run. Example: numeric, 10 or character "All", default = All.

Details

Specifically designed to reduce false positive CNVs and handle data from amplified DNA on dried blood spots.

Value

Data frame with the estimate copy number for each chromosome.

Author(s)

Marcelo Bertalan, Louise K. Hoeffding.

Source

http://biopsych.dk/iPsychCNV

Examples

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mockCNV <- MockData(N=5, Type="Blood", Cores=1)
cnvs <- CheckAbnChr(PathRawData=".", Cores=1, Pattern="^MockSample*", Skip=0)

mbertalan/iPsychCNV documentation built on June 30, 2017, 2:02 a.m.