bindcount {CSSP} | R Documentation |
Compute the number of reads overlapping the specified positions for the whole genome.
bindcount(chipdat, inputdat, bindpos, fragL = 200, whs = 250)
chipdat |
A list of the starting coordinates for aligned reads for all chromosomes, with positive numbers representing the 5' strand and negative numbers representing the 3' strand. |
inputdat |
A list of the starting coordinates for aligned reads for the input sample for all chromosomes, with positive numbers representing the 5' strand and negative numbers representing the 3' strand. |
bindpos |
A list of genome coordinates for each chromosome whose numbers of covering tags are computed. |
fragL |
A numeric value for the fragment length of the aligned reads. Default: 200. |
whs |
A numeric value for the half window size around the binding position. All tags overlapping this region are counted. Default: 250. |
A list of the number of overlapping tags for all position. Each list is a data.frame corresponding to a single chromosome, containing:
chip | The number of ChIP sample reads overlapping each position. |
input | The number of input sample reads overlapping each position. |
Chandler Zuo zuo@stat.wisc.edu
data( tagdat_input ) data( tagdat_chip ) data( bindpos ) bindcount( tagdat_chip, tagdat_input, bindpos, fragL = 100, whs = 300 )