readSeq: Wrapper for managing the reading of different raw data...

In SeqCNVCBS: Scan Statistics for CNV Detection with CBS

Description

This is a wrapper function. It calls one of the subroutines to reads in a datafile, depending on the format

Usage

readSeq(filename, formatName)

Arguments

filename	The file name of the data file to be read
formatName	The format the file is in. Can be one of the following. 'Chiang', 'ELANDPaired', 'JShen', 'MLove'. However, the last two are internal testing formats that should not be used.

Details

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. In case of paired read, we only use the front read (whichever has a smaller position label) and ask that you use only that for input.

Value

seqF	Read position for each read
seqChr	Chromosome of each mapped read

Author(s)

Jeremy J. Shen

References

Chiang et al., Nature Methods, 2009, Vol.6 No.1

See Also

readSeq, readSeqChiang, readSeqELANDPaired

Examples

# 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.