How to understand the output of plotRap function in ChIPQC package?
Hi, I am learning the ChIPQC package, and I fail to understand the Counts In Peaks plot (output of plotRap). From the vignette enter link description here :
What does each data point on the boxplot stand for? According to the description, this is the number of reads that fall in a peak. If so, this means that the number of data points in the boxplot is identical to the number of reads; however then the boxplot would actually show the distribution of the pileup values.
Is that correct?
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Pre-filtering in DESeq2 vignette
written by dylannicoembros •
-
colour background on lables from EnhancedVolcano in R
written by Astrid •
-
Interpreting time-series analysis with DESeq2 output
written by arshad1292 •
-
A question on Homer normalization
written by Aspire
-
Does DiffBind correctly designate peaks with very small fold-change to be significant
written by Aspire
-
ChIPQC error when running example from documentation
written by DBScan •
-
Exceptionally high peak/reads in ATACseq bam and peak files
written by bright602 •
-
Why pileup values of MACS2 output have decimal values?
written by Aspire
-
Does Chromvar require bulk ATAC-seq?
written by jmah •
-
Tool: ChIPQC: a package for assessing quality of ChIP-seq samples and experiments
written by Rory Stark
