Man pages for matthiasheinig/seqQTL
Package for preprocessing sequencing based traits for QTL analysis
| bed2GR | Read genomic ranges from bed files (zero based coordinates) |
| countBamInGRanges | Count reads from a bam file in genomic ranges |
| coverageBamInGRanges | Coverage profile from a bam file across genomic ranges |
| extract | Helper function to extract text using regular expressions |
| get.count.matrix | Get a count matrix from bam files that match a certain... |
| get.htseq.count.matrix | Get a count matrix from htseq-count files that match a... |
| get.rpkm | Normalize to reads per kilobase per million sequences |
| gff2GR | Read gene annotations in gff format |
| GR2gff | Export GRanges to gff format |
| GR2gtf | Export GRanges to gtf format |
| gtf2GR | Read gene annotations in gtf format |
| macs2GRange | Transform a MACS output peakfile into a GRanges object |
| makeGffAttributes | Helper function to generate the gff attributes field |
| makeGtfAttributes | Helper function to generate the gtf attributes field |
| merge.peaks | Merge MACS peaks calls from files in a directory |
| plot.spp.qc | Plot SPP quality metrics |
| seqQTL | Package for preprocessing sequencing based traits for QTL... |
| spp.qc.summary | Summary of SPP quality metrics from files in a directory |
