scChIPseqFromBam: Simulator of scChIP-seq read counts from alignment files

In plbaldoni/scChIPseqsim: Single-cell ChIP-seq Data Simulator Based on Pseudo-bulk Profiles

Description

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Usage

scChIPseqFromBam(
  label,
  path,
  genome,
  bamFile,
  binSize,
  baseSeqDepth,
  nCells,
  relSeqDepthPerCell,
  noisePerCell,
  chromosome = "chr19",
  basebinSize = 250,
  outputRanges = TRUE,
  excludeRegions = FALSE,
  shuffleChunks = 5000,
  shuffleProp = 0
)

Arguments

label	a character with the data label
path	a character with the path where the simulated data will be saved
genome	a character specifying the target genome
bamFile	a character specifying the path of the target alignment file
binSize	integer with the size of the bin window
baseSeqDepth	integer with the baseline sequencing depth for all simulated cells
nCells	integer with the number of cells to simulate
relSeqDepthPerCell	vector of size nCells with positive scalars representing the cell-specific relative sequencing depth with respect to baseSeqDepth. For instance, if relSeqDepthPerCell=rep(1,nCells) then all cells are simulated with an equal expected sequencing depth.
noisePerCell	vector of size nCells with positive scalars representing the cell-specific noise relative to the cell-specific expected sequencing depth. For instance, if noisePerCell=rep(0.05,nCells) then 5 will be randomly assigned to any genomic bin (regardless if the bin is in a peak region or not).
chromosome	vector of chromosomes to consider from the specified genome. Default is 'chr1'
basebinSize	integer giving the base bin size to calculate the gold-standard set of peaks. It must be smaller than binSize. Default 250
outputRanges	a logical indicating whether (TRUE) or not (FALSE) to save the binned coordinates of the genome. Default is TRUE
excludeRegions	a logical indicating whether to exclude blacklisted and gap regions or not. Default if FALSE
shuffleChunks	either NULL or an integer specifying the width of the size of the chunks to shuffle. If an integer, it must be divisible by basebinSize
shuffleProp	either NULL or the proportion of the genome to be shuffled

Details

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Value

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Author(s)

Pedro L. Baldoni, [e-mail]

plbaldoni/scChIPseqsim documentation built on June 11, 2020, 7:41 p.m.