get_array_input {iCNV}R Documentation

Get array information from given format

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.')

[Package iCNV version 1.6.0 Index]