CPsite_estimation {InPAS} | R Documentation |
estimate the cpsites for a giving chromosome
CPsite_estimation(chr.cov, utr3, MINSIZE, window_size, search_point_START, search_point_END, cutStart, cutEnd, adjust_distal_polyA_end, background, z2s, coverage_threshold, long_coverage_threshold, PolyA_PWM, classifier, classifier_cutoff, shift_range, depth.weight, genome, step=1, two_way=FALSE, tmpfolder=NULL, silence=TRUE)
chr.cov |
coverage list for one chromosome |
utr3 |
output of utr3Annotaion |
MINSIZE |
min size of short form |
window_size |
window size |
search_point_START |
search start point |
search_point_END |
search end point |
cutStart |
cut from start |
cutEnd |
cut from end |
adjust_distal_polyA_end |
adjust distal site or not |
background |
how to get the local background |
z2s |
output of zScoreThrethold |
coverage_threshold |
cutoff value for coverage |
long_coverage_threshold |
cutoff value for long form |
PolyA_PWM |
polyA PWM |
classifier |
classifier |
classifier_cutoff |
classifier cutoff |
shift_range |
shift range |
depth.weight |
output of depthWeight |
genome |
a BSgenome object |
step |
adjust step, default 1, means adjust by each base by cleanUpdTSeq. |
two_way |
Search the proximal site from both direction or not. |
tmpfolder |
temp folder could save and reload the analysis data for resume analysis. |
silence |
report progress or not. default not report. |
a data.frame
Jianhong Ou
CPsites
, searchProximalCPs
,
proximalAdj
,
proximalAdjByPWM
, proximalAdjByCleanUpdTSeq
,
PAscore
,PAscore2