View source: R/processHICdata.R
getHIContactCounts | R Documentation |
This function imports HIC reads and construct contact matrix based on user defined resolution or a number of required genomic bins.
getHIContactCounts(
bamfile,
region = NULL,
min.mapq = 10,
nbins = NULL,
resolution = NULL,
bsgenome = NULL
)
bamfile |
Bamfile with aligned reads. |
region |
If only a subset of the genomic regions should be loaded. |
min.mapq |
Minimum mapping quality when importing from BAM files. |
nbins |
A number of required bins to split selected genomic region into. |
resolution |
A |
A data.frame
object with HiC contact counts between two genomic region in each row.
David Porubsky
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