Doesn't DESeqDataSetFromMatrix work with data.frame only? It wouldn't work with
Spark's DataFrame - try collect(countMat) and others to convert them into
data.frame?
_____________________________
From: roni <[email protected]>
Sent: Thursday, February 18, 2016 4:55 PM
Subject: cannot coerce class "data.frame" to a DataFrame - with spark R
To: <[email protected]>
Hi , I am trying to convert a bioinformatics R script to use
spark R. It uses external bioconductor package (DESeq2) so the only conversion
really I have made is to change the way it reads the input file.
When I call my external R library function in DESeq2 I get error
cannot coerce class "data.frame" to a DataFrame .
I am listing my old R code and new spark R code below and the line
giving problem is in RED. ORIGINAL R - library(plyr)
library(dplyr) library(DESeq2)
library(pheatmap) library(gplots) library(RColorBrewer)
library(matrixStats) library(pheatmap)
library(ggplot2) library(hexbin) library(corrplot)
sampleDictFile <- "/160208.txt" sampleDict <-
read.table(sampleDictFile)
peaks <- read.table("/Atlas.txt") countMat <-
read.table("/cntMatrix.txt", header = TRUE, sep = "\t")
colnames(countMat) <- sampleDict$sample
rownames(peaks) <- rownames(countMat) <- paste0(peaks$seqnames, ":",
peaks$start, "-", peaks$end, " ", peaks$symbol) peaks$id <-
rownames(peaks) ############ # SPARK R
CODE peaks <- (read.csv("/Atlas.txt",header = TRUE, sep =
"\t"))) sampleDict<- (read.csv("/160208.txt",header = TRUE, sep
= "\t", stringsAsFactors = FALSE)) countMat<-
(read.csv("/cntMatrix.txt",header = TRUE, sep = "\t"))
-------------------------------------------------------------------
COMMON CODE for both -
countMat <- countMat[, sampleDict$sample] colData
<- sampleDict[,"group", drop = FALSE] design <- ~ group
dds <- DESeqDataSetFromMatrix(countData = countMat, colData
= colData, design = design)
This line gives error - dds <-
DESeqDataSetFromMatrix(countData = countMat, colData = (colData), design =
design) Error in DataFrame(colData, row.names = rownames(colData)) :
cannot coerce class "data.frame" to a DataFrame
I tried as.data.frame or using DataFrame to wrap the defs , but no
luck. What Can I do differently?
Thanks Roni
