| proximalAdjByCleanUpdTSeq {InPAS} | R Documentation |
adjust the proximal CP sites by cleanUpdTseq
proximalAdjByCleanUpdTSeq(idx.list, cov_diff.list, seqnames, starts, strands,
genome, classifier, classifier_cutoff,
shift_range, search_point_START, step=1)
idx.list |
the offset of positions of CP sites |
cov_diff.list |
the SSE values |
seqnames |
sequence names |
starts |
starts |
strands |
strands |
genome |
a BSgenome object |
classifier |
cleanUpdTSeq classifier |
classifier_cutoff |
cutoff value of the classiffier |
shift_range |
the searching range for the better CP sites |
search_point_START |
just in case there is no better CP sites |
step |
adjust step, default 1, means adjust by each base by cleanUpdTSeq. |
the step for calculating is 10, can not do every base base it is really very slow.
the offset of positions of CP sites after filter
Jianhong Ou
proximalAdjByPWM, proximalAdj,
PAscore2