cytof_clusterStat: Statistics of the cluster relusts

In haoeric/cytofkit_devel: cytofkit: an integrated mass cytometry data analysis pipeline

Description

Calculate the mean or median expression level of each marker for each cluster, or percentage of cell numbers of each cluster for each sample.

Usage

cytof_clusterStat(data, markers, cluster = "cluster", sample,
  statMethod = c("mean", "median", "percentage", "NULL"))

Arguments

data	Input data frame.
markers	The names of markers used for calcualtion.
cluster	The column name contatining cluster labels.
sample	The samples used for calculation.
statMethod	Statistics contatining mean, median or percentage.

Value

A matrix of the satatistics results

Examples

m1 <- c(rnorm(300, 10, 2), rnorm(400, 4, 2), rnorm(300, 7))
m2 <- c(rnorm(300, 4), rnorm(400, 16), rnorm(300, 10, 3))
m3 <- c(rnorm(300, 16), rnorm(400, 40, 3), rnorm(300, 10))
m4 <- c(rnorm(300, 7, 3), rnorm(400, 30, 2), rnorm(300, 10))
m5 <- c(rnorm(300, 27), rnorm(400, 40, 1),rnorm(300, 10))
c <- c(rep(1,300), rep(2,400), rep(3,300))
rnames <- paste(paste('sample_', c('A','B','C','D'), sep = ''), 
rep(1:250,each = 4), sep='_') 
exprs_cluster <- data.frame(cluster = c, m1 = m1, m2 = m2, m3 = m3, m4 = m4, m5 = m5)
row.names(exprs_cluster) <- rnames
cytof_clusterStat(data = exprs_cluster, cluster = "cluster", statMethod = "mean")

haoeric/cytofkit_devel documentation built on May 17, 2019, 2:29 p.m.