infinity_renameOutputs: Rename the outputs of infinityFlow to something more helpful...

In NKInstinct/flowHelpers: Personal Helper Functions for Cytometry Analysis

Rename the outputs of infinityFlow to something more helpful than concat.fcs

Description

Annoyingly, all infinityFlow concatenated files are output as 'concat.fcs', making it very difficult to use them in downstream analysis software like Seurat or CATALYST. This function renames them the name of their infinityOutput directory so that adding them to some downstream process doesn't throw errors later.

Usage

infinity_renameOutputs(
  parentDir,
  pattern = "\\.fcs$",
  concat_tag_to_remove = "FCS/concatenated",
  prefix = NULL,
  trialRun = TRUE
)

Arguments

parentDir	a filepath to the directory containing both the infinityOutput and pregated directories.
pattern	a regular expression that will be used to find the output files. The default of "\.fcs" works if you have only output a single concatenated file, but you'll need to be more specific if your infinityOutput also includes non-concatenated .fcs files (or any other .fcs for that matter, since the directories must be searched recursively).
concat_tag_to_remove	a regular expression showing what string to remove from the filename. The default will work if your infinityOutput only has a concatenated file in it.
prefix	a string to add in front of the filename for each renamed file. Pasted directly on, so if you want a specific separater, add it here. The default (NULL) pastes no string. Adding a prefix is useful if you are going to be combining several batches of samples with similar naming strategies (WT1, WT2, etc).
trialRun	Boolean. If true, this function will return a list of old and new filepaths but won't actually change them. You can either then run file.rename yourself using the old and new paths, or rerun with trialRun = FALSE to actually rename the files.

Value

Nothing - this modifies the filenames in place, so be careful! It's hard to undo this, hence the trialRun option to make sure it's working as intended before hitting go.

NKInstinct/flowHelpers documentation built on March 17, 2023, 1:42 a.m.