ConsensusPeak
is an R Package for calling consensus peaks from multiple
biological replicates. We implement several methods for thresholding, including
IDR conservative, IDR optimal, MSPC and ChIP-R.
if(!require("remotes")) install.packages("remotes")
remotes::install_github("neurogenomics/ConsensusPeak")
Load example data:
rep_treat_1 <- system.file("extdata",
"r1_creb_chr22.bam",
package = "ConsensusPeak")
rep_treat_2 <- system.file("extdata",
"r2_creb_chr22.bam",
package = "ConsensusPeak")
Run MACS3 peak calling and IDR thresholding with a single command:
result <- idr_analysis(treat_files = c(rep_treat_1, rep_treat_2),
control_files = NULL,
type = "conservative",
is_paired = FALSE, # Is the data paired-end?
idr_stringent = TRUE # Threshold at 0.01 or 0.05
out_dir = ".", # Directory to write the output files
nomodel = TRUE # MACS3 setting
)