medianByClusterMarker: Calculate median values of markers for each cluster

In fionarhuang/treeclimbR: An algorithm to find optimal signal levels in a tree

Calculate median values of markers for each cluster

Description

Calculate median value of each marker in each cluster.

Usage

medianByClusterMarker(
  SE,
  assay = 1,
  marker_in_column = TRUE,
  column_cluster = "cluster_id",
  use_marker = NULL
)

Arguments

SE	A SummarizedExperiment object.
assay	A numeric index or assay name indicating with assay of SE to use to calculate medians.
marker_in_column	A logical scalar, indicating whether markers (genes, features) are in the columns of SE or not.
column_cluster	The name of the column of colData(SE) that contains the cluster assignment of each sample.
use_marker	A logical or numeric vector such that SE[use_marker, ] (if marker_in_column = FALSE) or SE[, use_marker] (if marker_in_column = TRUE) subsets SE to the markers that should be retained. If NULL (default), all markers are used.

Value

A SummarizedExperiment object containing the median value of each marker in each cluster.

Author(s)

Ruizhu Huang, Charlotte Soneson

Examples

suppressPackageStartupMessages({
    library(SummarizedExperiment)
})

## Simulate data with 100 cells and 10 markers (5 type, 5 state markers)
set.seed(1)
count <- matrix(rpois(n = 1000, lambda = 10), nrow = 100)
colnames(count) <- paste0("mk", 1:10)
rowD <- data.frame("cluster" = sample(seq_len(6), 100, replace = TRUE))
colD <- data.frame(type_marker = rep(c(FALSE, TRUE), each = 5))

## SE with markers in columns
d_se <- SummarizedExperiment(assays = list(counts = count),
                             rowData = rowD,
                             colData = colD)
medianByClusterMarker(SE = d_se, marker_in_column = TRUE,
                      column_cluster = "cluster",
                      use_marker = colData(d_se)$type_marker)

## SE with markers in rows
d_se <- SummarizedExperiment(assays = list(counts = t(count)),
                             rowData = colD,
                             colData = rowD)
medianByClusterMarker(SE = d_se, marker_in_column = FALSE,
                      column_cluster = "cluster",
                      use_marker = rowData(d_se)$type_marker)

fionarhuang/treeclimbR documentation built on May 19, 2024, 1:18 p.m.