positionInfoContent: Get median information content for a given position
In omarwagih/siftr: generate SIFT scores directly in R
Description
Usage
Arguments
Value
Description
Get sequences that have no gap or X in position i,
compute median information content accross all positions
Usage
1
positionInfoContent(position = 1, aln_mat, frq, small_sample_correction = F)
Arguments
position
alignment position of interest
aln_mat
alignment matrix generated from letterMatrix
frq
precomputed amino acid frequency in the proteome
small_sample_correction
TRUE if small sample correction is applied
to information content calculation (not implemented currently, sift has it but doesn't use it)
Value
information content value between 0 (conserved) to log2(20) (least conserved)
omarwagih/siftr documentation built on May 24, 2019, 1:50 p.m.
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Description Usage Arguments Value
Description
Get sequences that have no gap or X in position i, compute median information content accross all positions
Usage
1 | positionInfoContent(position = 1, aln_mat, frq, small_sample_correction = F)
|
Arguments
position |
alignment position of interest |
aln_mat |
alignment matrix generated from letterMatrix |
frq |
precomputed amino acid frequency in the proteome |
small_sample_correction |
TRUE if small sample correction is applied to information content calculation (not implemented currently, sift has it but doesn't use it) |
Value
information content value between 0 (conserved) to log2(20) (least conserved)
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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