SeqListSCOPe {localScore} | R Documentation |
Several sequences
Description
A vector of character strings
Usage
SeqListSCOPe
Format
A list of 285 character strings with their entry codes as names
Source
Structural Classification Of Proteins database (SCOP). More precisely this data contain the 285 protein sequences of the data called "CF_scop2dom_20140205aa" with length from 31 to 404.
Examples
data(SeqListSCOPe)
head(SeqListSCOPe)
SeqListSCOPe[1]
nchar(SeqListSCOPe[1])
summary(sapply(SeqListSCOPe, nchar))
data(HydroScore)
MySeqScoreList=lapply(SeqListSCOPe, FUN=CharSequence2ScoreSequence, HydroScore)
head(MySeqScoreList)
AA=automatic_analysis(sequences=MySeqScoreList, model='iid')
AA[[1]]
# the p-value of the first 10 sequences
sapply(AA, function(x){x$`p-value`})[1:10]
# the 20th smallest p-values
sort(sapply(AA, function(x){x$`p-value`}))[1:20]
which(sapply(AA, function(x){x$`p-value`})<0.05)
table(sapply(AA, function(x){x$`method`}))
# The maximum sequence length equals 404 so it here normal that the exact method is used for
# all the 606 sequences of the data base
# Score distribution learnt on the data set
scoreSequences2probabilityVector(MySeqScoreList)
[Package localScore version 1.0.11 Index]