plotreg {iSeq} | R Documentation |
A function used to plot enriched genomic regions.
plotreg(gpos,ipct,conct,peak,col=c("yellow","green","grey0","blue"))
gpos |
A n by 2 matrix or data frame. The rows correspond to genomic bins. The first and second columns contain the start and end positions of the genomic windows/bins, respectively. |
ipct |
A n by 2 matrix containing the ChIP tag counts corresponding to the bins in gpos. ipct[,1] contains the counts for the chain 1 (usually the forward chain); ipct[,2] contains the counts for the chain 2 (usually the reverse chain). |
conct |
A n by 2 matrix containing the control tag counts corresponding to the bins in gpos. ipct[,1] contains the counts for the chain 1 (usually the forward chain); ipct[,2] contains the counts for the chain 2 (usually the reverse chain). |
peak |
A vector containing the peak (center) positions of the genomic regions. |
col |
The colors used to fill the rectangles. col[1] is used for ipct[,1], col[2] for ipct[,2], col[3] for conct[,1] and col[4] for conct[,2], respectively. |
No value returned.
Qianxing Mo qianxing.mo@moffitt.org
Qianxing Mo. (2012). A fully Bayesian hidden Ising model for ChIP-seq data analysis. Biostatistics 13(1), 113-28.
iSeq1
, iSeq2
, peakreg
,mergetag
#see the example in iSeq1