summarise: Quantify DNA methylation and chromatin accessibility over...

In aljabadi/scnmtseq: integration of multiome HMA data

Description

These functions overlap the individual CpG sites with genomic features such as promoters, gene bodies, etc.

Usage

summarise_sample(
  filepath,
  annotation_file,
  anno_name,
  context = c("CG", "GC"),
  valid_chromosomes = as.character(c(1:22, "MT", "X", "Y")),
  a = 0,
  b = 0,
  out.dir,
  force = FALSE
)

summarise_anno(
  samplefiles.path,
  annotation_file,
  anno_name,
  context = c("CG", "GC"),
  valid_chromosomes = as.character(c(1:22, "MT", "X", "Y")),
  a = 0,
  b = 0,
  out.dir,
  cores = parallel::detectCores(),
  force = FALSE
)

summarise_context(
  samplefiles.path,
  annotation_files,
  context = c("CG", "GC"),
  valid_chromosomes = as.character(c(1:22, "MT", "X", "Y")),
  a = 0,
  b = 0,
  out.dir,
  cores = parallel::detectCores(),
  force = FALSE
)

summarise(
  datapath = "data",
  annotation_files,
  valid_chromosomes = as.character(c(1:22, "MT", "X", "Y")),
  a = 0,
  b = 0,
  force,
  cores = parallel::detectCores(),
  out.dir = "output/scnomeseq"
)

Arguments

filepath	path to cov.gz file
annotation_file	path to the annotation file that has c("chr","start","end","strand","id") columns
anno_name	Character, annotation name to use and add to the summarised table, e.g. 'Enhancer'
context	One of c('CG', 'GC')
valid_chromosomes	Character vector of chromosomes to keep. Must match the chromosome notation in the data
a, b	Beta prior parameters. See SN 1 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4117646/
out.dir	Output directory to save the tsv file. The output file will be of form: outdir/CpG_or_GpC/anno_name/cov_file_name.tsv
force	Logical, whether to overwrite even if the output file exists
samplefiles.path	path to all cov.gz files for a given context
cores	Integer, number of CPUS to use
annotation_files	Named character vector (name = 'path') where names will be used as annotation names
datapath	Path to the data. It includes datapath/CpG and datapath/GpC subdirectories which contain the cov files for all cells

Details

• summarise_sample summarises the calls for a given cov.gz file and annotation file

• summarise_anno summarises the calls for a given annotation file for all cells

• summarise_context summarises the calls for a all annotation file for all cells for a given context (CG or GC)

• summarise summarises the calls for a all annotation file for all cells for both contexts (CG and GC)

Value

Writes file to out.dir and returns NULL

aljabadi/scnmtseq documentation built on Dec. 19, 2021, 1:30 a.m.