copar.Miner: ChIP-seq Information Mining & Process.
In gladex/COPAR: ChIP-seq Optimal Peak AnalyzeR

Description Usage Arguments Author(s) References Examples

copar.Miner is the package function to data process and the optimal peak candiate from the raw ChIP-seq input data (in BED format).

copar.Miner(input = "SRR015350_copa.rda",
           plotPN = T,
           plotFDR = T,
           maxPN = T)

`input`	The input file processed by copar.Aligner, e.g. input = "SRR015350_copa.rda".
`plotPN`	If plotPN==TRUE, copar.Miner will generate a heatmap of TIFF format for all peak number candidates.
`plotFDR`	If plotFDR==TRUE, copar.Miner will generate a heatmap of TIFF format for all corresponding False Discovery Rate (FDR) candidates.
`maxPN`	If maxPN==TRUE, copar.Miner will report the optimal peak count candiate.

Binhua Tang <bh.tang@outlook.com>

1. Tang B, Hsu H-K, Hsu P-Y, Bonneville R, Chen S-S, Huang TH-M, et al. Hierarchical modularity in ER¦Á transcriptional network is associated with distinct functions and implicates clinical outcomes. NPG Scientific Reports. 2012;2.

library(COPAR)
## check the help docs.
?copar.Miner
## run copar.Miner
copar.Miner(input = "SRR015350_copa.rda",
            plotPN = TRUE,
            plotFDR = TRUE,
            maxPN = TRUE)