Re: cannot coerce class "data.frame" to a DataFrame - with spark R

[roni]

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 
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 
> Sent: Thursday, February 18, 2016 4:55 PM
> Subject: cannot coerce class "data.frame" to a DataFrame - with spark R
> To: 
>
>
>
> 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
>
>
>
>

Re: cannot coerce class "data.frame" to a DataFrame - with spark R

[Felix Cheung]

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 
Sent: Thursday, February 18, 2016 4:55 PM
Subject: cannot coerce class "data.frame" to a DataFrame - with spark R
To:  


   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