run_deeptools: Run Deeptools

In GrahamHamilton/pipelineTools: Pipeline Tools for NGS Sequence Analysis Pipelines

Run Deeptools

Description

Runs the deeptools suite of programs

Usage

run_deeptools(
  command = NULL,
  input = NULL,
  control = NULL,
  output = NULL,
  output.format = NULL,
  binsize = NULL,
  sample.names = NULL,
  gtf = NULL,
  region = NULL,
  before.region = NULL,
  region.bases = NULL,
  after.region = NULL,
  plotType = NULL,
  kmeans = NULL,
  effective.genome.size = NULL,
  normalization = NULL,
  scale.factors = NULL,
  threads = 10,
  parallel = FALSE,
  cores = 4,
  execute = TRUE,
  deeptools = NULL,
  version = FALSE
)

Arguments

command	deeptools command to run, at present can choose from bamCoverage, computeMatrix and plotHeatmap, required
input	List of files to be processed, required
control	List of input control files, for bamCompare only
output	Name of output directory
output.format	Output format, bigwig or bedgraph, default bigwig
binsize	Size of the bins, in bases, default 50
sample.names	list of the sample name
gtf	Path to the gtf file
region	Region of the genome to limit the operation to,format is chr:start:end
before.region	Distance upstream of the reference-point selected
region.bases	Distance in bases to which all regions will be fit
after.region	Distance downstream of the reference-point selected
plotType	Type of plot can select lines, fill, se, std, overlapped_lines or heatmap
kmeans	Number of kmeans clusters to compute.
effective.genome.size	The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded. A table of values is available here: http://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html
normalization	Possible choices: RPKM (Reads Per Kilobase per Million mapped reads), CPM (Counts Per Million mapped reads), BPM (Bins Per Million mapped reads, similar to TPM), RPGC (reads per genomic content)
scale.factors	Method to use to scale the samples. Possible choices: readCount, SES and None
threads	Number of threads for each instance of deeptools to use, default set to 10
parallel	Run in parallel, default set to FALSE
cores	Number of cores/threads to use for parallel processing, default set to 4
execute	Whether to execute the commands or not, default set to TRUE
deeptools	Path to the where the deeptools programs are sorted (usually /usr/local/bin), required
version	Returns the version number

Value

A list with the deeptools commands

Examples

## Not run: 

# Version
command <- "deeptools"

deeptools.cmd <- run_deeptools(command = command,
                               deeptools.path = path,
                               version = TRUE)
deeptools.cmd

# Bam to bigwig
command <- "bamCoverage"
input.names <- "list of input file paths"
output.dir <- "directoryname"
output.names <- "list of names for samples"

deeptools.cmd <- run_deeptools(command = command,
                               input = input,
                               output = output,
                               sample.names = sample.names,
                               deeptools = path)
deeptools.cmd

# Bigwig to matrix
command <- "computeMatrix"
gtf <- "path/to/gtf"
input.names <- "list of input file paths"
output.dir <- "directoryname"
output.names <- "list of names for samples"

deeptools.cmd <- run_deeptools(command = command,
                               input = matrix.lists,
                               output = output,
                               sample.names = output.names,
                               gtf = gtf,
                               # parallel = TRUE,
                               # cores = 6,
                               deeptools = path)
deeptools.cmd

# plot heatmap
command <- "plotHeatmap"
input.names <- "list of input file paths"
output.dir <- "directoryname"
output.names <- "list of names for samples"

deeptools.cmd <- run_deeptools(command = command,
                               input = input.names,
                               output = output.dir
                               sample.names = output.names,
                               # parallel = TRUE,
                               # cores = 6,
                               deeptools = path)
deeptools.cmd

## End(Not run)

GrahamHamilton/pipelineTools documentation built on Dec. 8, 2024, 3:53 p.m.