pssm400: PSSM400 feature
In PSSMCOOL: Features Extracted from Position Specific Scoring Matrix (PSSM)
Description
Usage
Arguments
Value
Note
Examples
Description
This function firstly normalizes PSSM Matrix by formula:
P-min(P)/max(P)-min(P) then for any standard amino acid specifies its
position in protein sequence whereby a sub-matrix from PSSM corresponding
to these positions will be extracted, then for this sub-matrix computes
colSums
of its columns to create a vector of length 20, eventually a feature vector of
length 400 will be obtained.
Usage
1
pssm400(pssm_name)
Arguments
pssm_name
name of PSSM Matrix file
Value
feature vector of length 400
Note
if a specific amino acid did not exist in protein then colSums of whole
PSSM is computed.
Examples
1
X<-pssm400(system.file("extdata","C7GQS7.txt.pssm",package="PSSMCOOL"))
PSSMCOOL documentation built on Jan. 4, 2022, 5:07 p.m.
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Description Usage Arguments Value Note Examples
Description
This function firstly normalizes PSSM Matrix by formula:
P-min(P)/max(P)-min(P) then for any standard amino acid specifies its
position in protein sequence whereby a sub-matrix from PSSM corresponding
to these positions will be extracted, then for this sub-matrix computes
colSums
of its columns to create a vector of length 20, eventually a feature vector of
length 400 will be obtained.
Usage
1 | pssm400(pssm_name)
|
Arguments
pssm_name |
name of PSSM Matrix file |
Value
feature vector of length 400
Note
if a specific amino acid did not exist in protein then colSums of whole
PSSM is computed.
Examples
1 | X<-pssm400(system.file("extdata","C7GQS7.txt.pssm",package="PSSMCOOL"))
|
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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