An R package for identifying differential features from ChIA-PET expierments.
Raw FASTQ read files can be preprocessed with the dnaloop
(https://github.com/aryeelab/dnaloop) software, a PyPi package that relies
on samtools, bedtools, cutadapt, and MACS2 to align reads,
call anchor peaks, and summarize PETs per sample in the ChIA-PET experiment.
To use the loopsMake function from a different preprocessing step,
have files X.loop_counts.bedpe,Y.loop_counts.bedpe,
Z.loop_counts.bedpe in bed_dir for samples = (X,Y,Z) where the
first lines should resemble:
1 10002272 10004045 10 120968807 120969483 . 1
1 10002272 10004045 10 99551498 99552470 . 1
1 10002272 10004045 1 10002272 10004045 . 17
where the first three columns specify the position (chr:start:stop) of the first anchor, the second three columns specify the position (chr:start:stop) of the secnd anchor, the 7th column is "." and the 8th column is the number of paired-end reads support that particular PET.
We read in data from the preprocessing pipeline using the loopsMake
function. The example in the vignette uses sample data included in the diffloopdata
package.
Check out the vignette for a working example on quality control, visualization, association, and annotation