Usage
buildCIM(HiCFile, segFile, format, outputPrefix, resolution, header = FALSE,
inclusive = FALSE, verbose = TRUE, combineToSingle = TRUE)
Arguments
HiCFile
The name of the Hi-C file.
See for example: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM455134
segFile
The name of the segmentation file. The file provides the genomic coordinates
of each region. It should be a tab delimited file with the following columns:
chormosome, start, end, giving the chromosome name, start and end positions of
each region.
format
The format of the Hi-C file, taking one of the following values: "nodup",
"maq" or "sam"
outputPrefix
The prefix of the output files generated by this function. Each file is
appended with the name of the 2 chromosomes, that correspond to the output
contact map.
resolution
An integer value specifying the resolution of the given segmentation, if applicable.
Specifically, if the segmentation file defines regions of the same size
(for example: 1000000)
this variable should be set accordingly. Otherwise it should be set to -1.
Note that specifying the resolution greatly improves processing times.
header
optional: a boolean specifying whether the segmentation file includes a
header or not. Set to FALSE by default
inclusive
optional: a boolean specifying whether the segmentation is inclusive.
(i.e. whether the end position of one region overlaps with the start position
of the next region). Set to FALSE by default.
verbose
optional: a boolean specifying whether to report on the progress of the CIM build.
Set to TRUE by default.
combineToSingle
optional: a boolean specifying whether to also combine all the pairwise matrices
into a single matrix and write it to a file.If set to TRUE, an additional file
will be written, depending on available memory. Set to TRUE by default.