dot-summarizeHist: Summarize the histogram of strand proportions from the input...

In UofABioinformaticsHub/strandCheckR: Calculate strandness information of a bam file

Description

Summarize the histogram of positive proportions from the input windows obtained from the function getStrandFromBamFile

Usage

.summarizeHist(windows, split = c(10L, 100L, 1000L), breaks = 100L,
  useCoverage = FALSE, groupBy = NULL, normalizeBy = NULL)

Arguments

windows	data frame containing the strand information of the sliding windows. Windows can be obtained using the function getStrandFromBamFile.
split	an integer vector that specifies how you want to partition the windows based on the coverage. By default split = c(10,100,1000), which means that your windows will be partitionned into 4 groups, those have coverage < 10, from 10 to 100, from 100 to 1000, and > 1000
breaks	an integer giving the number of bins for the histogram
useCoverage	if TRUE then plot the coverage strand information, otherwise plot the number of reads strand information. FALSE by default
groupBy	the column names of windows that will be used to group the data
normalizeBy	instead of using the raw read count/coverage, we will normalize it to a proportion by dividing it to the total number of read count/coverage of windows that have the same value in the normalizeBy columns.

Value

a dataframe object

See Also

getStrandFromBamFile, plotHist, plotWin

UofABioinformaticsHub/strandCheckR documentation built on Aug. 15, 2021, 9:08 a.m.