View source: R/13.search_distalCPs.R
search_distalCPs | R Documentation |
search distal CP sites
search_distalCPs(
chr.cov.merge,
conn_next_utr3,
curr_UTR,
window_size,
depth.weight,
long_coverage_threshold,
background,
z2s
)
chr.cov.merge |
merged coverage data for a given chromosome |
conn_next_utr3 |
A logical(1) vector, indicating whether joint to next
3UTR or not (used by |
curr_UTR |
GRanges of 3' UTR for a given chromosome |
window_size |
An integer(1) vector, the window size for novel distal or proximal CP site searching. default: 100. |
depth.weight |
A named vector. One element of an output of
|
long_coverage_threshold |
An integer(1) vector, specifying the cutoff threshold of coverage for the terminal of long form 3' UTRs. If the coverage of first 100 nucleotides is lower than coverage_threshold, that transcript will be not considered for further analysis. Default, 2. |
background |
A character(1) vector, the range for calculating cutoff threshold of local background. It can be "same_as_long_coverage_threshold", "1K", "5K","10K", or "50K". |
z2s |
one element of an output of |
a list #'
dCPs, a data frame converted from GRanges
chr.cov.merge, depth-normalized sample/condition specific coverage
next.exon.gap, all-in-one collapsed, refined next.exon.gap coverage
annotated.utr3,all-in-one collapsed coverage for annotated proximal UTRs
Jianhong Ou
get_PAscore2()
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