I am adding gene names to my results from DESeq2
however, I am running into a problem and don't know how to fix it
I am getting the hgnc_symblo column as <logical> and with NA values
here is the code
res_cisp$ensembl <- sapply(strsplit(rownames(res_cisp), split="\\+"),"[",1)
ensembl <- useMart("ensembl", dataset="mmusculus_gene_ensembl", host="uswest.ensembl.org" )
ensembl
genemap <- getBM(attributes=c("ensembl_gene_id", "entrezgene_id", "hgnc_symbol"),
filters= "ensembl_gene_id",
values= res_cisp$ensembl,
mart= ensembl)
idx <- match(res_cisp$ensembl, genemap$ensembl_gene_id)
res_cisp$entrez <- genemap$entrezgene_id[idx]
res_cisp$hgnc_symbol <- genemap$hgnc_symbol[idx]
head(res_cisp)
and the results
log2 fold change (MMSE): condition cisplatin it saline vs naive
Wald test p-value: condition cisplatin.it.saline vs naive
DataFrame with 6 rows and 8 columns
baseMean log2FoldChange lfcSE
<numeric> <numeric> <numeric>
ENSMUSG00000103377 49.1110927570198 0.00414782875544946 0.49189537354036
ENSMUSG00000098104 12.2865163125002 -0.073818230097171 0.460767651597771
ENSMUSG00000102175 7.18534311588583 -0.204118906299468 1.1017255901118
ENSMUSG00000103265 14.3593112522462 0.0176820483747342 0.664184999715962
ENSMUSG00000103922 50.0663878879066 0.317321233753418 0.388894551120162
ENSMUSG00000033845 4150.26363804658 0.408154062125359 0.251104088928333
pvalue padj ensembl entrez
<numeric> <numeric> <character> <integer>
ENSMUSG00000103377 0.980115594258496 0.996217945158712 ENSMUSG00000103377 NA
ENSMUSG00000098104 0.707277000946448 0.89484074550068 ENSMUSG00000098104 NA
ENSMUSG00000102175 NA NA ENSMUSG00000102175 NA
ENSMUSG00000103265 0.847547508190696 0.951328475392166 ENSMUSG00000103265 NA
ENSMUSG00000103922 0.189685601646874 0.486707535702066 ENSMUSG00000103922 NA
ENSMUSG00000033845 0.0532513850609968 0.235103096130907 ENSMUSG00000033845 27395
hgnc_symbol
<logical>
ENSMUSG00000103377 NA
ENSMUSG00000098104 NA
ENSMUSG00000102175 NA
ENSMUSG00000103265 NA
ENSMUSG00000103922 NA
ENSMUSG00000033845 NA
any ideas?
sessionInfo() R version 3.6.1 (2019-07-05) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Sierra 10.12.5
Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale: [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods
[9] base
other attached packages:
[1] biomaRt2.42.0 DESeq21.26.0 SummarizedExperiment1.16.1
[4] DelayedArray0.12.2 BiocParallel1.20.1 matrixStats0.55.0
[7] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.0
[10] IRanges2.20.2 S4Vectors0.24.3 BiocGenerics0.32.0
[13] dplyr0.8.5 tibble2.1.3 magrittr_1.5
loaded via a namespace (and not attached):
[1] bitops1.0-6 bit640.9-7 RColorBrewer1.1-2
[4] progress1.2.2 httr1.4.1 tools3.6.1
[7] backports1.1.5 utf81.1.4 R62.4.1
[10] rpart4.1-15 Hmisc4.3-1 DBI1.1.0
[13] colorspace1.4-1 nnet7.3-13 tidyselect1.0.0
[16] gridExtra2.3 prettyunits1.1.1 bit1.1-15.2
[19] curl4.3 compiler3.6.1 cli2.0.2
[22] htmlTable1.13.3 scales1.1.0 checkmate2.0.0
[25] genefilter1.68.0 askpass1.1 rappdirs0.3.1
[28] stringr1.4.0 digest0.6.25 foreign0.8-76
[31] XVector0.26.0 base64enc0.1-3 jpeg0.1-8.1
[34] pkgconfig2.0.3 htmltools0.4.0 dbplyr1.4.2
[37] htmlwidgets1.5.1 rlang0.4.5 rstudioapi0.11
[40] RSQLite2.2.0 acepack1.4.1 RCurl1.98-1.1
[43] GenomeInfoDbData1.2.2 Formula1.2-3 Matrix1.2-18
[46] Rcpp1.0.3 munsell0.5.0 fansi0.4.1
[49] lifecycle0.2.0 stringi1.4.6 zlibbioc1.32.0
[52] BiocFileCache1.10.2 grid3.6.1 blob1.2.1
[55] crayon1.3.4 lattice0.20-40 splines3.6.1
[58] annotate1.64.0 hms0.5.3 locfit1.5-9.1
[61] knitr1.28 pillar1.4.3 geneplotter1.64.0
[64] XML3.99-0.3 glue1.3.1 latticeExtra0.6-29
[67] data.table1.12.8 BiocManager1.30.10 png0.1-7
[70] vctrs0.2.4 gtable0.3.0 openssl1.4.1
[73] purrr0.3.3 assertthat0.2.1 ggplot23.3.0
[76] xfun0.12 xtable1.8-4 survival3.1-11
[79] AnnotationDbi1.48.0 memoise1.1.0 cluster_2.1.0
thanks,
ooohh thank you!!!!!