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Add in functionality for CPAT3 #275

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Add in functionality for CPAT3 #275

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f05ea8a
Update analyze_external_sequence_analysis.R
mpage21 Mar 12, 2025
28e4500
Update analyze_external_sequence_analysis.R
mpage21 Mar 12, 2025
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32 changes: 31 additions & 1 deletion R/analyze_external_sequence_analysis.R
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Original file line number Diff line number Diff line change
Expand Up @@ -124,6 +124,36 @@ analyzeCPAT <- function(
}


} else if (ncol(myCPATresults) == 11) { # Handling CPAT3
temp <- myCPATresults$seq_ID
myCPATresults <- myCPATresults[, c(3, 8, 9, 10, 11)] # Extract 'mRNA', 'ORF', 'Fickett', 'Hexamer', 'Coding_prob'
myCPATresults$id <- temp
if (!all(
colnames(myCPATresults) %in% c(
"mRNA",
"ORF",
"Fickett",
"Hexamer",
"Coding_prob",
"id"
)
)) {
stop(
'There seems to be a problem with the CPAT3 result file. Please check it is the right file and try again'
)
}
# rename to match the expected format
colnames(myCPATresults) <-
c(
'mRNA_size',
'ORF_size',
'Fickett_score',
'Hexamer_score',
'coding_prob',
'id'
)


} else {
stop(
'There seems to be a problem with the CPAT result file. Please check it is the rigth file and try again'
Expand Down Expand Up @@ -2862,4 +2892,4 @@ analyzeDeepTMHMM <- function(
}

return(switchAnalyzeRlist)
}
}