readInput: Manage reading and merging of raw datasets. Main file input

In SeqCNVCBS: Scan Statistics for CNV Detection with CBS

Description

This is used to control the read of a meta file containing names of data files, merge, and give usable output for the main program

Usage

readInput(inputFilename, formatName="Chiang", sep = "\t")

Arguments

inputFilename	The name of file, containing relevant information of all input files
formatName	The format in which the data files are written in. We use the simple 'Chiang' as default format of input.
sep	Delimiter of the meta input file, default is tab-delimited

Details

The meta input file should be organized in a table format with 2 columns, one of which is 'file' and the other is 'type', indicating the data file names and whether the data is from normal or tumor.

Value

normalSeq	A list containing the combined normal/control reads
tumorSeq	A list containing the combined case/tumor reads

Author(s)

Jeremy J. Shen

See Also

readListInputFile, readSeq

Examples

# This shows the format of the meta file
data(JSSim_Meta)
print(JSSim_Meta)

# This shows the recommended format, the Chiang data format
data(JSSim_NormalSim1)
print(head(JSSim_NormalSim1))

SeqCNVCBS documentation built on May 2, 2019, 6:51 p.m.