View source: R/15.adjust_proximalCPsByNBC.R
adjust_proximalCPsByNBC | R Documentation |
adjust the proximal CP sites by using Naive Bayes classifier from cleanUpdTSeq
adjust_proximalCPsByNBC(
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 MSE values |
seqnames |
a character(n) vector, the chromosome/scaffolds' names |
starts |
starts |
strands |
strands |
genome |
a BSgenome::BSgenome object |
classifier |
cleanUpdTSeq classifier |
classifier_cutoff |
cutoff value of the classifier |
shift_range |
the searching range for the better CP sites |
search_point_START |
just in case there is no better CP sites |
step |
adjusting 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
adjust_proximalCPsByPWM()
, get_PAscore2()
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