Thanks Felix .
I tried that but I still get the same error . Am I missing something?
dds <- DESeqDataSetFromMatrix(countData = collect(countMat), colData =
collect(colData), design = design)
Error in DataFrame(colData, row.names = rownames(colData)) :
cannot coerce class "data.frame" to a DataFrame
On Thu, Feb 18, 2016 at 9:03 PM, Felix Cheung <felixcheun...@hotmail.com>
wrote:
> 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 <roni.epi...@gmail.com>
> Sent: Thursday, February 18, 2016 4:55 PM
> Subject: cannot coerce class "data.frame" to a DataFrame - with spark R
> To: <user@spark.apache.org>
>
>
>
> 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
>
>
>
>
