jianhong / cleanupdtseq Goto Github PK

There is a bug in

 baseOnly = TRUE)[, -5])

should be changed to

 baseOnly = TRUE)[, -5, drop = FALSE])

Reccently, I use cleanUpdTSeq to filter the internal primed events. it run well on test data, but for real data(PAS-seq, polyA-seq, 3'-seq, etc), it is very slow and speed nearly a day for a sample. are there any method to improve this？ the following are my running code
`library('cleanUpdTSeq')

Args <- commandArgs()
input_file <- Args[6]
output_file <- Args[7]
#cat(Args)

testSet <- read.table(input_file, sep = "\t", header = T)
peaks <- BED2GRangesSeq(testSet, upstream.seq.ind=7,
downstream.seq.ind=8, withSeq=TRUE)
testSet.NaiveBayes <- buildFeatureVector(peaks,
upstream=40, downstream=30,
wordSize=6, alphabet=c("ACGT"),
sampleType="unknown",
replaceNAdistance=30,
method="NaiveBayes",
ZeroBasedIndex=1, fetchSeq=FALSE)

data(classifier)
test_results <- predictTestSet(testSet.NaiveBayes=testSet.NaiveBayes,
classifier=classifier,
outputFile=NULL,
assignmentCutoff=0.5)

test_results <- test_results[test_results[2] < 0.5, 1]
write.table(test_results, output_file, quote = F, row.names = F, col.names = F)`

Thank you very much and looking forward to your reply