scan.sequence: identify TFBS hits in the sequence(s)
In matthuska/tRap: A biophysical model for transcription factor binding affinities
Description
Usage
Arguments
Value
Description
Identify TFBS exceeding the given P-value (or affinity) cutoff
Usage
1
scan.sequence(seq, pwm, matrix.name, pvalue.cutoff, affinity.cutoff = NULL)
Arguments
seq
character vector with sequences to scan
pwm
the position weight matrix
matrix.name
name of the transfac matrix
pvalue.cutoff
significance threshold for the TFBS hits
affinity.cutoff
score threshold (default NULL)
Value
a matrix with 4 columns: seq, start, end, affinity containing the positions of significant hits
matthuska/tRap documentation built on May 21, 2019, 1:23 p.m.
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Description Usage Arguments Value
Description
Identify TFBS exceeding the given P-value (or affinity) cutoff
Usage
1 | scan.sequence(seq, pwm, matrix.name, pvalue.cutoff, affinity.cutoff = NULL)
|
Arguments
seq |
character vector with sequences to scan |
pwm |
the position weight matrix |
matrix.name |
name of the transfac matrix |
pvalue.cutoff |
significance threshold for the TFBS hits |
affinity.cutoff |
score threshold (default NULL) |
Value
a matrix with 4 columns: seq, start, end, affinity containing the positions of significant hits
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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