readall_tab: Load wiggle data
In hochwagenlab/hwglabr: Collection of R functions used in the Hochwagen Lab

readall_tab

R Documentation

Load wiggle data

Description

This function allows you to load tab-separated wiggle data. Adapted from function written by Tovah Markowitz (original function name: readAll.tab).

Usage

readall_tab(fileLocation, useReadr = TRUE, progressBar = TRUE,
  localCopy = FALSE, asBedGraph = FALSE)

Arguments

`fileLocation`	A string with the path to the folder containing the wiggle data. No default.
`useReadr`	Boolean indicating whether to use the much faster `read_tsv()` from Hadley Wickham's readr package instead of base R's `read.table`. Defaults to `TRUE`.
`progressBar`	Boolean indicating whether to display a progress bar (using R package pbapply). Defaults to `TRUE`.
`localCopy`	Boolean indicating whether to create local copy of target files before reading data. If `TRUE` a local folder is automatically created and deleted after use. Use this argument to avoid reading files directly from shared locations (namely LabShare). Defaults to `FALSE`.
`asBedGraph`	Boolean indicating whether to return the data in bedGraph-like format instead of R list of 16 data frames. Genomic coordinates are kept as 1-based. Defaults to `FALSE`.

Value

Either an R list of 16 data frames, one for each chromosome (asBedGraph=FALSE) or a bedGraph-like data frame (asBedGraph=TRUE).

Examples

## Not run: 
readall_tab("/Path/to/wiggles/folder/Red1_WT_reps_SacCer3_2mis_MACS_wiggle_norm/")
readall_tab("/Path/to/wiggles/", useReadr = TRUE, progressBar = TRUE)
readall_tab("/Path/to/wiggles/", useReadr = T, progressBar = T, localCopy = T)
#' readall_tab("/Path/to/wiggles/", asBedgraph = TRUE)

## End(Not run)

hochwagenlab/hwglabr documentation built on Feb. 25, 2025, 5:41 a.m.