seqCBS (version 1.2.1)

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

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 either 'Chiang' or 'ELANDPaired'. We recommend using Chiang since this is the minimal required format.

Value

seqF

Read position for each read

seqChr

Chromosome of each mapped read

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. If one has paired read, please use only one of the reads and the mapped location should be the 5'-end.

References

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

See Also

readSeq, readSeqChiang, readSeqELANDPaired

Examples

# NOT RUN {
# This shows the recommended format, the Chiang data format
data(JSSim_NormalSim1)
print(head(JSSim_NormalSim1))
# }