align_fastq_to_vdjca: align_fastq_to_vdjca
In debdagybra/IMIabgd: Analyze Tcells data with mixcr and vdjtools

Description Usage Arguments Value Author(s)

execute the command : 'align -OvParameters.geneFeatureToAlign=VTranscript

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align_fastq_to_vdjca(java_param = "java -Xmx4g -Xms3g -jar", path_mixcr,
  input_dir, input_filename, output_filename = "auto",
  report_name = "alignmentReport", replace = FALSE, string_only = FALSE)

`java_param`	a character string containing java parameters
`path_mixcr`	the path to mixcr.jar
`input_dir`	where the files are
`input_filename`	file name (type R1.fastq.gz), (with or without the extension)
`report_name`	the name of the file alignmentReport. (without the extension) Set to NULL to not create the file.
`replace`	if TRUE, if the output file already exists, it will be replaced.
`string_only`	if TRUE, don't execute the command but returns it in a string

run command line in console. Creates .vdjca files in the same directory than the fastq.gz files Returns the name of the outputfile if string_only=FALSE Returns command if string_only=TRUE

DEBOT Damien <damien.debot@gmail.com>

debdagybra/IMIabgd documentation built on May 21, 2019, 12:19 p.m.