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

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

Value

normalSeq

A list containing the combined normal/control reads

tumorSeq

A list containing the combined case/tumor reads

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. We recommend using the 'Chiang' format, as used by the datasets of Chiang (2009). This format requires minimal memory and contains all relevant information for this program. It is a table with two columns, first being the chromosome of the mapped read, and the second being the position of the read in the chromosome. One line for each observation.

Examples

Run this code

# NOT RUN {
# 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))
# }