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

Description Usage Arguments Value See Also

View source: R/summarizeHist.R

Description

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

Usage

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summarizeHist(windows, split = c(10, 100, 1000), breaks = 100,
useCoverage = FALSE, group_by = NULL, normalize_by = NULL)

Arguments

windows

data frame containing the strand information of the sliding windows. Windows can be obtained using the function getWinFromBamFile.

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

group_by

the column names of windows that will be used to group the data

normalize_by

the column names of windows that will be used to normalize the read count or read coverage into proportion

Value

a dataframe object

See Also

getWinFromBamFile, plotHist, plotWin


strandCheckR documentation built on Nov. 1, 2018, 2:26 a.m.