Description Usage Arguments Examples
Title
1 2 3 4 5 6 7 8 | readJunctionSeqCounts(countfiles = NULL, countdata = NULL, samplenames,
design, flat.gff.file = NULL, test.formula1 = formula(~sample + countbin +
condition:countbin), analysis.type = c("junctionsAndExons", "junctionsOnly",
"exonsOnly"), nCores = 1, use.exons = NULL, use.junctions = NULL,
use.known.junctions = TRUE, use.novel.junctions = TRUE,
use.multigene.aggregates = FALSE, gene.names = NULL, verbose = TRUE,
method.countVectors = c("geneLevelCounts", "sumOfAllBinsForGene",
"sumOfAllBinsOfSameTypeForGene"), noDESeqMatrix = FALSE)
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noDESeqMatrix |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 | dir.name="/Volumes/Bioinformatics$/2015/Nimer_Cheng/"
file.sample="decoder.bySample.txt"
file.count="_junction_seq_new_gtf_7/QC.spliceJunctionAndExonCounts.forJunctionSeq.txt"
file.gff="Mus_musculus.GRCm38.83.JunctionSeq.flat.gff"
path.file.sample<-paste0(dir.name,file.sample)
decoder.bySample<-read.table(path.file.sample,header=T,stringsAsFactors = F)
print(decoder.bySample)
#Get count file
path.file.count<-paste0(dir.name,decoder.bySample$sample.ID,file.count)
countFiles<-paste0(path.file.count)
print(countFiles)
#Get annotation file
flat.file.gff<-paste0(dir.name,file.gff)
print(flat.file.gff)
method.countVectors = c("geneLevelCounts","sumOfAllBinsForGene","sumOfAllBinsOfSameTypeForGene")
method.countVectors <- match.arg(method.countVectors)
jscs = readJunctionSeqCounts(countfiles = as.character(sample.files),
samplenames = sample.names,
design = Re,
flat.gff.file = flat.gff.file,
verbose = verbose,
use.junctions = use.junctions,
use.novel.junctions = use.novel.junctions,
use.known.junctions = use.known.junctions,
use.exons = use.exons,
use.multigene.aggregates = use.multigene.aggregates,
nCores = nCores,
method.countVectors = method.countVectors,
test.formula1 = test.formula1,
gene.names = gene.names
)
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