generic.compass.wrapper: COMPASS Wrapper

In seshadrilab/flowHelpers: Collection of helper functions for analyzing FCM data

Description

This function runs COMPASS once for each of the unique values defined by the uniqueruns argument (if provided)

Usage

generic.compass.wrapper(path = NULL, seed = NULL, outdir = NULL,
  cnode = NULL, nodemarkermap = NULL, individuals = NULL,
  grouping = NULL, uniqueruns = NULL, lineplotxvar = NULL,
  iter = 40000, lineplotgroupby = NULL, countFilterThreshold = 0)

Arguments

path	The path to the folder in which the GatingSetList or GatingSet is saved
seed	(Optional) Number to set seed to [default NULL]
outdir	Directory in which to save output, e.g. heatmaps
cnode	Node on which to run COMPASS
nodemarkermap	List mapping nodes to marker names
individuals	pData column containing individual identifiers (rows of heatmap)
grouping	(Optional) pData columns on which to group rows in heatmap, as a character vector [default NULL]
uniqueruns	(Optional) pData column identifying unique runs. Use if you need multiple runs. [default NULL]
lineplotxvar	(Optional) pData column which defines groups along x-axis in FS-score line plot, e.g. Time [default NULL]
iter	(Optional) Number of COMPASS iterations to perform on each repitition (8 repetitions total) [default 40,000]
lineplotgroupby	(Optional) This should be specified if lineplotxvar is given. pData column which defines which values to connect in the line plot (usually something like "PTID")

Value

Nothing

Examples

## Not run: 
generic.compass.wrapper(path="/home/path/to/GatingSetList",
                        seed=1,
                        outdir="/path/to/OutDirectory",
                        cnode="8+",
                        nodemarkermap=list("8+/154+" = "CD154",
                                           "8+/IFNg+" = "IFNg",
                                           "8+/IL4+" = "IL4",
                                           "8+/TNFa+" = "TNFa",
                                           "8+/IL22+" = "IL22",
                                           "8+/IL17+" = "IL17a",
                                           "8+/IL2+" = "IL2"),
                        individuals="PATIENT ID",
                        uniqueruns="Peptide")
                        
## End(Not run)

seshadrilab/flowHelpers documentation built on May 23, 2019, 4:05 a.m.