Trajectory-based differential expression analysis for single-cell sequencing data
tradeSeq tradeSeq workflow using input from From slingShot
Workflow using input from Monocle
Example code importing only counts pseudotime and cells weights on each trajectory
#! /usr/bin/Rscript library(tradeSeq) library(monocle) library(RColorBrewer) library(SingleCellExperiment) library(slingshot) palette(brewer.pal(8, "Dark2")) packageDescription("tradeSeq")$Version #load data cellPSMatrix <- as.matrix(read.table("Subset.PsTime.txt", sep="\t")) cellWeights <- as.matrix(read.table("Subset.CellsWeight.txt", sep="\t")) counts <- as.matrix(read.table("RawCounts.txt", sep="\t")) #this step is optional #select the subset of cells that are present on the pseudotime and cells weight file countsFiltered <- subset.matrix(counts, select=rownames(cellWeights)) #Evaluate the knots that we'll use when fitting the General Additive Models icMat <- evaluateK(counts = countsFiltered, k = 3:10, nGenes = 200, verbose = T, pseudotime = cellPSMatrix, cellWeights = cellWeights) library(BiocParallel) library(magrittr) # Register BiocParallel Serial Execution (no parallelization in that case) BiocParallel::register(BiocParallel::SerialParam()) FitModels <- fitGAM(counts = countsFiltered,nknots = 8, pseudotime = cellPSMatrix, cellWeights = cellWeights ) patternRes <- patternTest(FitModels) oPat <- order(patternRes$waldStat, decreasing = TRUE) head(rownames(patternRes)[oPat]) save.image("Data_afterPatternTest.RData") pdf( "plotSmoothers.pdf", w=11, h=8.5) plotSmoothers(FitModels, countsFiltered , gene = rownames(patternRes)[oPat][1]) plotSmoothers(FitModels, countsFiltered , gene = rownames(patternRes)[oPat][2]) plotSmoothers(FitModels, countsFiltered , gene = rownames(patternRes)[oPat][3]) plotSmoothers(FitModels, countsFiltered , gene = rownames(patternRes)[oPat][4]) plotSmoothers(FitModels, countsFiltered , gene = rownames(patternRes)[oPat][5]) dev.off() write.table(patternRes, file="PatternTest8knots.txt", sep="\t", quote=F, row.names=T)
Example of input files:
Note:
See TracWiki
for help on using the wiki.