plotAvgProf2 failed

[songeric1107]

ChIPseeker::plotAvgProf2(peak1,TxDb = txdb, conf = 0.95, by = "gene", type = "body",weightCol = "V5",ignore_strand = F)

preparing promoter regions... 2021-12-08 03:25:48 PM preparing tag matrix... 2021-12-08 03:25:48 PM plotting figure... 2021-12-08 03:25:51 PM Error in getTagCiMatrix(tagMatrix, conf = conf, ...) : unused arguments (by = "gene", type = "body", ignore_strand = F)

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[MingLi-929]

plotAvgProf2 <- function(peak, weightCol = NULL, TxDb = NULL,
                         upstream = 1000, downstream = 1000,
                         xlab = "Genomic Region (5'->3')",
                         ylab = "Peak Count Frequency",
                         conf,
                         facet = "none",
                         free_y = TRUE,
                         verbose = TRUE, 
                         ignore_strand = FALSE,
                         ...)

plotAvgProf2() is inherited from the previous methods, which did not support to plot the body region. You should try plotPeakProf2() instead.

plotPeakProf2 <- function(peak, 
                          upstream, 
                          downstream,
                          conf,
                          by,
                          type,
                          weightCol = NULL, 
                          TxDb = NULL,
                          xlab = "Genomic Region (5'->3')",
                          ylab = "Peak Count Frequency",
                          facet = "none",
                          free_y = TRUE,
                          verbose = TRUE, 
                          nbin = NULL,
                          ignore_strand = FALSE,
                          ...)