Changes between Version 1 and Version 2 of SOP/scRNA-seq/tradeSeq

Timestamp:

10/27/20 15:27:49 (5 years ago)

Author:

ibarrasa

Comment:

--

SOP/scRNA-seq/tradeSeq

@@ -5 +5 @@
 [https://github.com/statOmics/tradeSeq tradeSeq GitHub page] 
 
-[https://github.com/statOmics/tradeSeq--- Input from From slingShot] 
+[https://bioconductor.org/packages/devel/bioc/vignettes/tradeSeq/inst/doc/tradeSeq.html#load-data tradeSeq tradeSeq workflow using input from From slingShot] 
 
-[https://github.com/statOmics/tradeSeq--- Input from From Monocle] 
+[https://statomics.github.io/tradeSeq/articles/Monocle.html Workflow using input from Monocle] 
 
-Example code 
+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)
+RNGversion("3.5.0")
+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)
+
+
+}}}
+