cytof_clusterStat: Statistics of the cluster results

In JinmiaoChenLab/cytofkit2: cytofkit2: an integrated mass cytometry data analysis pipeline. Cytofkit provides functions for data pre-processing, fast clustering, data visualization through linear or non-linear dimensionality reduction, automatic identification of cell subsets, and inference of the relatedness between cell subsets

Statistics of the cluster results

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 containing mean, median or percentage.

Value

A matrix of the statistics 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")

JinmiaoChenLab/cytofkit2 documentation built on May 12, 2022, 8:09 a.m.