subsetSC: Load in methylation data

In rhondabacher/methylscaper: Visualization of Methylation Data

Load in methylation data

Description

This function loads the single-cell files. It takes a path to the data files and a chromosome number as arguments and returns the desired subset of the data. Processing by chromosome is important for speed and memory efficiency. The input files should be tab separated with three columns. The first column is the chromosome, the second is the position (basepair), and the third is the methylation indicator/rate. The folder should contain two subfolders titled met and acc, with the endogenous methylation and accessibility methylation files, respectively.

Usage

subsetSC(
  path,
  chromosome,
  startPos = NULL,
  endPos = NULL,
  updateProgress = NULL
)

Arguments

path	Path to the folder containing the single-cell files.
chromosome	The chromosome to subset the files to.
startPos	The index of the first position to include in the subsetting. This is optional as further narrowing of the position can be done in the visualization step/tab. In the Shiny app, a slider will let the user refine the positions.
endPos	The index of the final position to include in subset.
updateProgress	A function for generating progress bars in the Shiny app. Should be left NULL otherwise.

Value

The output is RDS files that can be loaded into the visualization tab on the Shiny app

Examples

# example not run since needs directory input from user
# subsc.out <- subsetSC("filepath", chromosome=19)

rhondabacher/methylscaper documentation built on Oct. 10, 2024, 8:18 a.m.