runCreateMx: Run Create Matrix

In RGLab/HIPCMatrix: Microarray and RNA-seq Processing for ImmuneSpace

Run Create Matrix

Description

Runs all steps of creating matrix in ImmuneSpace.

Usage

runCreateMx(
  study,
  matrix_name,
  selected_biosamples,
  fas_id,
  labkey.url.base = "https://datatools.immunespace.org/",
  base_dir = file.path("/share", "files", "Studies", study, "@files"),
  output_dir = file.path(base_dir, "analysis", "exprs_matrices"),
  analysis_dir = file.path(base_dir, "rawdata", "gene_expression"),
  debug_dir = file.path(analysis_dir, "create-matrix", matrix_name),
  taskOutputParams = NULL,
  verbose = TRUE,
  snapshot = TRUE,
  reload = TRUE
)

Arguments

study	Study accession
matrix_name	Name of the matrix
selected_biosamples	String listing biosample accessions to include, separated by commas (should be from one cell type from one cohort)
fas_id	Feature Annotation Set ID
labkey.url.base	labkey.url.base
base_dir	Base directory for all analysis and output files. If output_dir, analysis_dir, debug_dir are not defined, they will be created under base_dir. When running in the HIPCMatrix module on ImmuneSpace servers, this should be the same as pipeline.root.
output_dir	Directory to write final matrices. On ImmuneSpace servers: /share/files/Studies/<study_accession>/@files/analysis/exprs_matrices
analysis_dir	Directory to write intermediate files. On servers, /share/files/Studies/<study_accession>/@files/rawdata/gene_expression
debug_dir	Directory to write debug files. On servers, it will be the same as analysis.directory in the HIPCMatrix pipeline,
taskOutputParams	taskOutputParams
verbose	Print verbose debug statements?
snapshot	write copies of source files to debug_dir?
reload	Force re-download of supplementary files from GEO?

RGLab/HIPCMatrix documentation built on Jan. 29, 2023, 5:13 a.m.