load_data: Load Dataset Containing Copy Number Profile

In yun-feng/WGDAP: Whole Genome Duplication Analysis Pipeline

Description

Read text files containing copy number profiles called for multiple samples.

Usage

load_data(mainDir, cancer_type, coor = "coords.txt")

Arguments

mainDir	The directory which contains all the files.
cancer_type	The type of the cancer: the files are named as "cancer_type"_minorcn.csv or "cancer_type"_majorcn.csv
coor	The name for the coordinate file. Default as coords.txt.

Details

There are three different csv files containing minor copy, major copy and coordinates.

This returns list containing all the input data we need for down-stream analysis. The list consists of two values, which indicate the number of samples and loci respectively, and three data frame which contain minor copy, major copy, and coordinates.

Value

A list containing: the number of samples, number of loci, all minor copies, all major copies, all loci

Examples

wkdata<-load_data("C:\\Double","BLCA")

yun-feng/WGDAP documentation built on Nov. 5, 2019, 1:22 p.m.