extract_citrus_clusters: This function extracts clusted flow cytometric expression...

Description Usage Arguments Details Value

View source: R/citrus_helper_functions.R

Description

1. to extract *all* CV.min clusters from the RDSfile, leave cluster_id=NULL mat_of_cvmin_clusters <- extract_citrus_clusters(""citrusOutput_10000cells/Age.rds", anno, markers)

Usage

1
extract_citrus_clusters(RDSfile, anno, cluster_id = NULL, markers = markers)

Arguments

RDSfile

path to the Citrus .rds file that contains the Citrus run (eg. "/path/to/Age.rds")

anno

data.frame containing annotation. anno <- read.csv("annotation.txt") in directory of each Citrus run

cluster_id

numeric id of the cluster to extract , if NULL then extract all cv.min clusters found in RDS

markers:

named list translating markers <-> channels

Details

2. to extract a particular cluster from the RDSfile, specify its cluster_id mat_of_cluster12345 <- extract_citrus_clusters(""citrusOutput_10000cells/Age.rds", anno, cluster_id=12345, markers)

Value

a named list of expression matrices (list has length 1 if you specified a single cluster, option 2 above)


RGLab/flowIncubator documentation built on Jan. 27, 2018, 2:48 p.m.