mergeQCdataRDS: mergeQCdataRDS

In plantformatics/Socrates: Analysis of scATAC-seq data

mergeQCdataRDS

Description

This function merges QC data RDS objects. Useful for joining replicates and multiple samples for downstream analysis. obj simple way to aggregate multiple samples into obj single socrates object is to move all the samples of interest into obj directory and load the paths with list.files. IMPORTANT - only merge RDS objects where the same bins/peaks were used for each of the objects. The easiest way to ensure mergeable objects is to use the same window size (instead of ACRs) for the function generateMatrix. Use this function for rds objects saved from QC analysis. The function mergeSocratesRDS should be specifically used for objects produced using convertSparseData.

Usage

mergeQCdataRDS(filenames)

Arguments

filenames

Named vector of filepaths.

specify input files

input.files <- list.files(pattern="*.rds", path="/path/to/rds/directory")input.files1 "rep1.rds" "rep2.rds"

name the input files

names(input.files) <- c("rep1", "rep2")input.filesrep1 rep2"rep1.rds" "rep2.rds"

merge reps 1 and 2

merged.obj <- mergeQCdatRDS(filenames=input.files)

check data structure

str(merged.obj)

plantformatics/Socrates documentation built on April 3, 2025, 1:02 p.m.