get_array_input: Get array information from given format

In iCNV: Integrated Copy Number Variation detection

Description

If your array input file follow the format in the example, you could use this function to extract array LRR and baf. Remember to load library before hands. Save 4*[# of chr] lists, each list has N entry. N = # of individuals snp_lrr: SNP LRR intensity; snp_lrr.pos: the position of the SNPs snp_baf: the BAF of the SNPs; snp_baf.pos: the position of the SNPs

Usage

get_array_input(dir = character(), pattern = character(), chr = NULL,
  projname = "")

Arguments

dir	A string. The directory path to the folder where store signal intensity file according to chr. Type character
pattern	A string. The pattern of all the intensity file. Type character
chr	Specify the chromosome you want to generate. Must be of int from 1-22. If not specify, this function will generate files for all chromosomes. Default NULL
projname	Name of the project. Type character

Value

void

Examples

dir <- system.file("extdata", package="iCNV")
pattern <- paste0('*.csv.arrayicnv$')
get_array_input(dir,pattern,chr=22,projname='icnv.demo.')

iCNV documentation built on Nov. 8, 2020, 11:12 p.m.