testDiffExp: Perform post-hoc differential gene expression analysis

View source: R/testDiffExp.R

testDiffExpR Documentation

Perform post-hoc differential gene expression analysis

Description

This function will perform differential gene expression analysis within differentially abundant neighbourhoods, by first aggregating adjacent and concordantly DA neighbourhoods, then comparing cells within these aggregated groups for differential gene expression using the input design. For comparing between DA neighbourhoods see findNhoodMarkers.

Usage

testDiffExp(
  x,
  da.res,
  design,
  meta.data,
  model.contrasts = NULL,
  assay = "logcounts",
  subset.nhoods = NULL,
  subset.row = NULL,
  gene.offset = TRUE,
  n.coef = NULL,
  na.function = "na.pass"
)

Arguments

x

A Milo object containing single-cell gene expression and neighbourhoods.

da.res

A data.frame containing DA results, as expected from running testNhoods.

design

A formula or model.matrix object describing the experimental design for differential gene expression testing. The last component of the formula or last column of the model matrix are by default the test variable. This behaviour can be overridden by setting the model.contrasts argument. This should be the same as was used for DA testing.

meta.data

A cell X variable data.frame containing single-cell meta-data to which design refers. The order of rows (cells) must be the same as the Milo object columns.

model.contrasts

A string vector that defines the contrasts used to perform DA testing. This should be the same as was used for DA testing.

assay

A character scalar determining which assays slot to extract from the Milo object to use for DGE testing.

subset.nhoods

A logical, integer or character vector indicating which neighbourhoods to subset before aggregation and DGE testing (default: NULL).

subset.row

A logical, integer or character vector indicating the rows of x to use for sumamrizing over cells in neighbourhoods.

gene.offset

A logical scalar the determines whether a per-cell offset is provided in the DGE GLM to adjust for the number of detected genes with expression > 0.

n.coef

A numeric scalar refering to the coefficient to select from the DGE model. This is especially pertinent when passing an ordered variable and only one specific type of effects are to be tested.

na.function

A valid NA action function to apply, should be one of na.fail, na.omit, na.exclude, na.pass.

Details

Adjacent neighbourhoods are first merged based on two criteria: 1) they share at least overlap number of cells, and 2) the DA log fold change sign is concordant. This behaviour can be modulated by setting overlap to be more or less stringent. Additionally, a threshold on the log fold-changes can be set, such that lfc.threshold is required to merge adjacent neighbourhoods. Note: adjacent neighbourhoods will never be merged with opposite signs unless merge.discord=TRUE.

Within each aggregated group of cells differential gene expression testing is performed using the single-cell log normalized gene expression with a GLM (for details see limma-package), or the single-cell counts using a negative binomial GLM (for details see edgeR-package). When using single-cell data for DGE it is recommended to set gene.offset=TRUE as this behaviour adjusts the model by the number of detected genes in each cell as a proxy for differences in capture efficiency and cellular RNA content.

Value

A list containing a data.frame of DGE results for each aggregated group of neighbourhoods.

Author(s)

Mike Morgan & Emma Dann

Examples

data(sim_discrete)

milo <- Milo(sim_discrete$SCE)
milo <- buildGraph(milo, k=20, d=10, transposed=TRUE)
milo <- makeNhoods(milo, k=20, d=10, prop=0.3)

meta.df <- sim_discrete$meta
meta.df$SampID <- paste(meta.df$Condition, meta.df$Replicate, sep="_")
milo <- countCells(milo, meta.data=meta.df, samples="SampID")

test.meta <- data.frame("Condition"=c(rep("A", 3), rep("B", 3)), "Replicate"=rep(c("R1", "R2", "R3"), 2))
test.meta$Sample <- paste(test.meta$Condition, test.meta$Replicate, sep="_")
rownames(test.meta) <- test.meta$Sample
da.res <- testNhoods(milo, design=~Condition, design.df=test.meta[colnames(nhoodCounts(milo)), ])
da.res <- groupNhoods(milo, da.res, da.fdr=0.1)
nhood.dge <- testDiffExp(milo, da.res, design=~Condition, meta.data=meta.df)
nhood.dge


MikeDMorgan/miloR documentation built on Aug. 7, 2022, 8:21 a.m.