cytottest {cytofast} | R Documentation

## preform t-test on cfList

### Description

Performs a separate t-test on each cluster within a cfList. The output is added and can also be used by other functions

### Usage

    cytottest(cfList, group, adjustMethod, ...)

### Arguments

`cfList` | a cfList object. It should contain at least data in the 'counts' slot.
`group` | one of: a character vector referring to a column name in the `samples` slot of the `cfList`. a factor indicating the grouping for the t.test.
`adjustMethod` | character, correction method used in `p.adjust`, choose from `c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none")`. If omitted, no correction takes place.
`...` | further arguments passed on to `t.test`.

### Value

Returns a cfList with a 'results' slot.

### Examples

    # Read Data
    dirFCS <- system.file("extdata", package="cytofast")
    cfData <- readCytosploreFCS(dir = dirFCS, colNames = "description")

    # relabeling of clusterID
    levels(cfData@expr[,"clusterID"]) <- gsub("[^0-9]", "", levels(cfData@expr[,"clusterID"]))

    # Add cell counts to cfList and add meta data
    cfData <- cellCounts(cfData, frequency = TRUE, scale = TRUE)
    meta <- spitzer[match(row.names(cfData@samples), spitzer$CSPLR_ST),]
    cfData@samples <- cbind(cfData@samples, meta)

    # Run t-test
    cfData@samples$effect <- gsub("_D\\d", "", spitzer$group)
    cfData <- cytottest(cfData, group  = "effect", adjustMethod = "bonferroni")
    cfData@results

[Package cytofast version 1.0.0 Index]