Commit d59b1a3f authored by Holger Brandl's avatar Holger Brandl

cont. leipzig data processing

parent 8e1a31be
......@@ -37,4 +37,5 @@ makePcaPlot <- function(x = getData(), group = NA, items=rownames(x), title = ""
}
makePcaPlot(getData(30,4,2,distort = 0.7), getGroup(30,2))
## example
# makePcaPlot(getData(30,4,2,distort = 0.7))
#### Tophat Mapping Report from the logs
TophatMappingReport(){
## todo replace source with simple R script as for bowtie-report
echo '
devtools::source_url("http://dl.dropbox.com/u/113630701/rlibs/deepseq/ngs_tools.R")
createMappingReport()
' | R -q --vanilla
}
#### Bowtie Mapping Report from the logs
Bowtie2MappingReport(){
echo '
devtools::source_url("http://dl.dropbox.com/u/113630701/rlibs/base-commons.R")
logSuffix=".logs"
parseAlgnSummary <- function(alignSummary){
#alignSummary="./H2Az_Rep1_Lane1_Lib4454.bowtie.log"
algnData <- readLines(alignSummary)
data.frame(
condition=trimEnd(basename(alignSummary), logSuffix),
num_reads=as.numeric(str_split_fixed(algnData[3], " ", 2)[1]),
unique_mappers=as.numeric(str_split_fixed(str_trim(algnData[6]), " ", 2)[1]),
mapping_efficiency=as.numeric(str_replace(str_split_fixed(algnData[8], " ", 2)[1], "%", "")),
multi_mappers=as.numeric(str_split_fixed(str_trim(algnData[7]), " ", 2)[1])
)
}
mapStats <- ldply(list.files(".", logSuffix, full.names=TRUE, recursive=T), parseAlgnSummary, .progress="text")
write.delim(mapStats, file="mapStats.txt")
ggplot(melt(mapStats), aes(condition, value)) + geom_bar(stat="identity") +facet_wrap(~variable, scales="free") + ggtitle("mapping summary") + scale_y_continuous(labels=comma) + theme(axis.text.x=element_text(angle=90, hjust=0))
ggsave2(w=10, h=10, p="mapstats")
ggplot(mapStats, aes(condition, mapping_efficiency)) + geom_bar(stat="identity") +coord_flip() + ylim(0,100) + ggtitle("mapping efficiency")
ggsave2(p="mapstats")
ggplot(mapStats, aes(condition, num_reads)) + geom_bar(stat="identity") + coord_flip() + ggtitle("read counts")
ggsave2(p="mapstats")
ggplot(mapStats, aes(condition, unique_mappers)) + geom_bar(stat="identity") + coord_flip() + ggtitle("unique alignment") + scale_fill_discrete()
ggsave2(p="mapstats")
' | R --vanilla
}
export -f Bowtie2MappingReport
## create fastq report for all fastq and fastq.gz files in the current directory
mmFastqc(){
outputDir="fastqc_reports"
# filePattern="fastq.gz"
......@@ -17,3 +18,36 @@ mmFastqc(){
}
export -f mmFastqc
### Create a cuffdb on a network of lustre file-systen
MakeCuffdb() {
if [ $# -ne 2 ]; then echo "Usage: MakeCuffdb <gtffile> <genomebuild>"; return; fi
echo '
devtools::source_url("http://dl.dropbox.com/u/113630701/rlibs/base-commons.R")
options(width=150)
require.auto(cummeRbund)
createCuffDbTrickyDisk <- function(dbDir, gtfFile, genome, ...){
tmpdir <- tempfile()
system(paste("cp -r", dbDir, tmpdir))
oldWD <- getwd()
setwd(tmpdir)
cuff <- readCufflinks(rebuild=T, gtf=gtfFile, genome="mm10", ...)
# cuff <- readCufflinks(gtf=gtfFile, genome="mm10", rebuild=T)
system(paste("cp cuffData.db", dbDir))
system(paste("rm -r", tmpdir))
setwd(oldWD)
return(cuff)
}
gtfFile=commandArgs(TRUE)[1]
genomeBuild=commandArgs(TRUE)[2]
createCuffDbTrickyDisk(getwd(), gtfFile, genomeBuild)
' | R -q --no-save --no-restore --args $1 $2
}
export -f MakeCuffdb
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