Read count frequency around TSS

This function generates a plot of read count frequency around TSS.

tss_plot(
  peaklist,
  txdb = NULL,
  tss_distance = c(-3000, 3000),
  conf = 0.95,
  resample = 500,
  interact = FALSE,
  workers = check_workers()
)

Arguments

peaklist

A list of peak files as GRanges object. Files must be listed and named using list(). e.g. list("name1"=file1, "name2"=file2) If not named, default file names will be assigned.

txdb

A TxDb annotation object from Bioconductor.

tss_distance

A vector specifying the distance upstream and downstream around transcription start sites (TSS). The default value is c(-3000,3000); meaning peak frequency 3000bp upstream and downstream of TSS will be displayed.

conf

Confidence interval threshold estimated by bootstrapping (0.95 means 95 Argument passed to plotAvgProf.

resample

Number of bootstrapped iterations to run. Argument passed to plotAvgProf.

interact

Default TRUE. By default, plots are interactive. If set FALSE, all plots in the report will be static.

workers

Number of cores to parallelise bootstrapping across. Argument passed to plotAvgProf.

Value

A named list of profile plots.

Examples

### Load Data ###
data("CnT_H3K27ac") # example peaklist GRanges object
data("CnR_H3K27ac") # example peaklist GRanges object
### Create Named Peaklist ###
peaklist <- list("CnT"=CnT_H3K27ac, "CnR"=CnR_H3K27ac) 
my_plot <- tss_plot(peaklist = peaklist, 
                    tss_distance=c(-50,50),
                    workers = 1)
#> --- Running tss_plot() ---
#> Warning: >> TxDb is not specified, use 'TxDb.Hsapiens.UCSC.hg19.knownGene' by default...
#> >> Running bootstrapping for tag matrix...		 2024-10-18 02:21:02 PM 
#> >> Running bootstrapping for tag matrix...		 2024-10-18 02:21:02 PM 
#> Done.