Question: ChIPQC plots for input samples
0
23 months ago by
C T90
United States
C T90 wrote:

I have generated a QC report on my 35 samples (28 ChIP and 7 input samples) using:

ChIPQCreport(proj1.all,facet=F).

How do I generate plots with the corresponding input file on one graph?

For example: CCPlot seems to have all samples and only have 1 legend replicate.

My sample sheet and the plots generate can be downloaded from here: https://1drv.ms/f/s!Aiu_09KS3rmGi3zTZVMoE7X2nZIQ

chipqc • 368 views
modified 23 months ago by Thomas Carroll400 • written 23 months ago by C T90
Answer: ChIPQC plots for input samples
0
23 months ago by
United States/New York/The Rockefeller University
Thomas Carroll400 wrote:

hi,

Something like below (this uses package example data) should reproduce what you are after I believe.

data("tamoxifen_QC")

ChIPQCreport(tamoxifen,facetBy=c("Tissue","Condition"),colourBy = "Factor")

best,

tom

Faceting by tissue and color by factor gets me closer. However, it still do not plot the input. It's probably because I didn't specify the samples sheet correctly. So, in my samples sheet, I previously only listed my ChIP samples and in bamControls the path to the corresponding input bam file, so factors do not have inputs (this is samples.csv in the link above). I tried to add the input samples as additional rows (this is samples_v2.csv), however it gave me an error that each bam file must be associated with at most one peakset.

So, I think the problem is how do I specify input samples in the samples sheet?

Also, is there an easy way to reduce the fonts in the plots? and is there an easy way to get the NRF (non-redundant fraction) for all samples in a table?

Thanks!