Dear All,
I cannot get DEXseq to work with my data. I get the following error message: Error: could not find function "DEXSeqDataSetFromHTSeq"
I have tried to fix it by adding the function to the working session:
I imported (copied and paste into the terminal) the function DEXSeqDataSetFromHTSeq from a Github page (https://github.com/Bioconductor-mirror/DEXSeq). When I run it, with this function loaded, it then asks for another function - DEXSeqDataSet, so I add that... which then asks for Granges,so I load that... which then asks for matrixStats so I load that ... then it fails .. this cant be right!! I am using the latest DEXseq (see below). I updated all packages .... I generated the count files and exons gff on a server and imported the files to biolinux7 .
commands (without the extra functions for Github which didnt solve my problem) - commands got from the documentation:
inDir = '/home/peter/Desktop/exon_DE'
countFiles = list.files(inDir, pattern=".exon_counts$", full.names=TRUE)
basename(countFiles)
flattenedFile = list.files(inDir, pattern="gff$", full.names=TRUE)
basename(flattenedFile)
sampleTable = data.frame(row.names = c("N116_A17_1", "N116_A17_2", "N116_A17_3", "N116_D2A_1", "N116_D2A_2", "N116_D2A_3", "PS01_A17_1", "PS01_A17_2", "PS01_A17_3", "PS01_D2A_1", "PS01_D2A_2", "PS01_D2A_3"), condition = c("N116_A17", "N116_A17", "N116_A17", "N116_D2A", "N116_D2A", "N116_D2A", "PS01_A17", "PS01_A17", "PS01_A17", "PS01_D2A", "PS01_D2A", "PS01_D2A"),libType = c("paired-end", "paired-end", "paired-end", "paired-end", "paired-end", "paired-end", "paired-end", "paired-end", "paired-end", "paired-end", "paired-end", "paired-end"))
dxd =read.HTSeqCounts(countFiles,sampleData=sampleTable,design= ~ sample + exon + condition:exon,flattenedfile=flattenedFile)
library("DEXSeq")
dxd = DEXSeqDataSetFromHTSeq(countFiles,sampleData=sampleTable,design= ~ sample + exon + condition:exon,flattenedfile=flattenedFile)
I really hope someone can help me :)
cheers,
Pete
> sampleTable
condition libType
N116_A17_1 N116_A17 paired-end
N116_A17_2 N116_A17 paired-end
N116_A17_3 N116_A17 paired-end
N116_D2A_1 N116_D2A paired-end
N116_D2A_2 N116_D2A paired-end
N116_D2A_3 N116_D2A paired-end
PS01_A17_1 PS01_A17 paired-end
PS01_A17_2 PS01_A17 paired-end
PS01_A17_3 PS01_A17 paired-end
PS01_D2A_1 PS01_D2A paired-end
PS01_D2A_2 PS01_D2A paired-end
PS01_D2A_3 PS01_D2A paired-end
> countFiles
[1] "/home/peter/Desktop/exon_DE/
N116_A17_1.exon_counts"
[2] "/home/peter/Desktop/exon_DE/N116_A17_2.exon_counts"
[3] "/home/peter/Desktop/exon_DE/N116_A17_3.exon_counts"
[4] "/home/peter/Desktop/exon_DE/N116_D2A_1.exon_counts"
[5] "/home/peter/Desktop/exon_DE/N116_D2A_2.exon_counts"
[6] "/home/peter/Desktop/exon_DE/N116_D2A_3.exon_counts"
[7] "/home/peter/Desktop/exon_DE/PS01_A17_1.exon_counts"
[8] "/home/peter/Desktop/exon_DE/PS01_A17_2.exon_counts"
[9] "/home/peter/Desktop/exon_DE/PS01_A17_3.exon_counts"
[10] "/home/peter/Desktop/exon_DE/PS01_D2A_1.exon_counts"
[11] "/home/peter/Desktop/exon_DE/PS01_D2A_2.exon_counts"
[12] "/home/peter/Desktop/exon_DE/PS01_D2A_3.exon_counts"
$ more A.pisum_exons.gff
[ 2:40PM]
GL349621 dexseq_prepare_annotation.py aggregate_gene 7560 8108
. - . gene_id "1"
GL349621 dexseq_prepare_annotation.py exonic_part 7560 8108
. - . transcripts "1.1"; exonic_part_number "001"; gene_id "1"
GL349621 dexseq_prepare_annotation.py aggregate_gene 73684 88372
. - . gene_id "2"
GL349621 dexseq_prepare_annotation.py exonic_part 73684 73783
. - . transcripts "2.1"; exonic_part_number "001"; gene_id "2"
GL349621 dexseq_prepare_annotation.py exonic_part 85524 86737
. - . transcripts "2.1"; exonic_part_number "002"; gene_id "2"
GL349621 dexseq_prepare_annotation.py exonic_part 86840 88372
. - . transcripts "2.1"; exonic_part_number "003"; gene_id "2"
GL349621 dexseq_prepare_annotation.py aggregate_gene 108844 112984
. - . gene_id "3"
GL349621 dexseq_prepare_annotation.py exonic_part 108844 109785
. - . transcripts "3.1"; exonic_part_number "001"; gene_id "3"
GL349621 dexseq_prepare_annotation.py exonic_part 112937 112984
. - . transcripts "3.1"; exonic_part_number "002"; gene_id "3"
GL349621 dexseq_prepare_annotation.py aggregate_gene 123266 123583
. - . gene_id "4"
GL349621 dexseq_prepare_annotation.py exonic_part 123266 123583
. - . transcripts "4.1"; exonic_part_number "001"; gene_id "4"
> flattenedFile
[1] "/home/peter/Desktop/exon_DE/A.pisum_exons.gff"
> sessionInfo()
R version 3.2.4 (2016-03-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu precise (12.04.5 LTS)
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets
[7] methods base
other attached packages:
[1] matrixStats_0.50.2 GenomicRanges_1.12.5 IRanges_1.18.0
[4] DEXSeq_1.8.0 Biobase_2.22.0 BiocGenerics_0.8.0
loaded via a namespace (and not attached):
[1] XML_3.96-1.1 Biostrings_2.28.0 Rsamtools_1.12.4
[4] bitops_1.0-6 stats4_3.2.4 magrittr_1.5
[7] stringi_1.0-1 zlibbioc_1.6.0 hwriter_1.3.2
[10] statmod_1.4.24 tools_3.2.4 stringr_1.0.0
[13] biomaRt_2.16.0 RCurl_1.95-4.1
Warning messages:
1: multiple methods tables found for ‘as.vector’
2: multiple methods tables found for ‘is.unsorted’
3: multiple methods tables found for ‘append’
4: replacing previous import ‘BiocGenerics::append’ by ‘IRanges::append’ when loading ‘GenomicRanges’
5: replacing previous import ‘BiocGenerics::as.vector’ by ‘IRanges::as.vector’ when loading ‘GenomicRanges’
6: replacing previous import ‘BiocGenerics::is.unsorted’ by ‘IRanges::is.unsorted’ when loading ‘GenomicRanges’
7: replacing previous import ‘BiocGenerics::append’ by ‘IRanges::append’ when loading ‘Biostrings’
8: replacing previous import ‘BiocGenerics::as.vector’ by ‘IRanges::as.vector’ when loading ‘Biostrings’
9: replacing previous import ‘BiocGenerics::is.unsorted’ by ‘IRanges::is.unsorted’ when loading ‘Biostrings’
10: multiple methods tables found for ‘is.unsorted’
11: multiple methods tables found for ‘append’
