colTest: Perform a simple wilcoxon-rank-sum test or t-test on the...

In ellispatrick/spicyR: Spatial analysis of in situ cytometry data

Perform a simple wilcoxon-rank-sum test or t-test on the columns of a data frame

Description

Perform a simple wilcoxon-rank-sum test or t-test on the columns of a data frame

Usage

colTest(df, condition, type = NULL, feature = NULL, imageID = "imageID")

Arguments

df	A data.frame or SingleCellExperiment, SpatialExperiment
condition	The condition of interest
type	The type of test, "wilcox", "ttest" or "survival".
feature	Can be used to calculate the proportions of this feature for each image
imageID	The imageID's if presenting a SingleCellExperiment

Value

Proportions

Examples

# Test for an association with long-duration diabetes
# This is clearly ignoring the repeated measures...
data("diabetesData")
diabetesData <- spicyR:::.format_data(
  diabetesData, "imageID", "cellType", c("x", "y"), FALSE
)
props <- getProp(diabetesData)
condition <- spicyR:::getImagePheno(diabetesData)$stage
names(condition) <- spicyR:::getImagePheno(diabetesData)$imageID
condition <- condition[condition %in% c("Long-duration", "Onset")]
test <- colTest(props[names(condition), ], condition)

ellispatrick/spicyR documentation built on Dec. 20, 2024, 10:50 a.m.