This package provides the output of running Salmon on a set of 24 RNA-seq samples from Alasoo, et al. “Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response”, published in Nature Genetics, January 2018 doi: 10.1038/s41588-018-0046-7.
6 donors were selected from those that had publicly available reads in
ENA. The selection procress is recorded in the file
inst/scripts/ena_download.R, the donors were chosen as all female,
the sample having been received as frozen, and then the top 6 were
chosen based on mean purity as recorded by the study authors.
Salmon
version 0.12.0 was run using
Gencode
human reference transcripts v29, with a
snakemake
script that can be seen in inst/scripts/Snakemake and with
log output in inst/scripts/snakemake.log.
The quantification output is in the inst/extdata/quant
directory. The quant.sf files have been gzipped to preserve space,
so they are stored as quant.sf.gz. There are 20 Gibbs inferential
replicates for each sample.
The inst/scripts/ena_downloads.R R script also shows how the column
data file coldata.csv was generated. This file contains the
phenotypic information about the 24 samples:
dir <- system.file("extdata", package="macrophage")
coldata <- read.csv(file.path(dir,"coldata.csv"))
coldata <- coldata[,c(1,2,3,5)]
coldata
## names sample_id line_id condition_name
## 1 SAMEA103885102 diku_A diku_1 naive
## 2 SAMEA103885347 diku_B diku_1 IFNg
## 3 SAMEA103885043 diku_C diku_1 SL1344
## 4 SAMEA103885392 diku_D diku_1 IFNg_SL1344
## 5 SAMEA103885182 eiwy_A eiwy_1 naive
## 6 SAMEA103885136 eiwy_B eiwy_1 IFNg
## 7 SAMEA103885413 eiwy_C eiwy_1 SL1344
## 8 SAMEA103884967 eiwy_D eiwy_1 IFNg_SL1344
## 9 SAMEA103885368 fikt_A fikt_3 naive
## 10 SAMEA103885218 fikt_B fikt_3 IFNg
## 11 SAMEA103885319 fikt_C fikt_3 SL1344
## 12 SAMEA103885004 fikt_D fikt_3 IFNg_SL1344
## 13 SAMEA103885284 ieki_A ieki_2 naive
## 14 SAMEA103885059 ieki_B ieki_2 IFNg
## 15 SAMEA103884898 ieki_C ieki_2 SL1344
## 16 SAMEA103885157 ieki_D ieki_2 IFNg_SL1344
## 17 SAMEA103885111 podx_A podx_1 naive
## 18 SAMEA103884919 podx_B podx_1 IFNg
## 19 SAMEA103885276 podx_C podx_1 SL1344
## 20 SAMEA103885021 podx_D podx_1 IFNg_SL1344
## 21 SAMEA103885262 qaqx_A qaqx_1 naive
## 22 SAMEA103885228 qaqx_B qaqx_1 IFNg
## 23 SAMEA103885308 qaqx_C qaqx_1 SL1344
## 24 SAMEA103884949 qaqx_D qaqx_1 IFNg_SL1344
The package also contains a summarized experiment object created
using the script in inst/scripts/gse_create.R. This object can be
loaded with data("gse").
Thanks to the study authors for posting their data publicly and clearly labelling their data.
sessionInfo()
## R version 4.3.0 RC (2023-04-13 r84269)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.2 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.17-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: America/New_York
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## loaded via a namespace (and not attached):
## [1] compiler_4.3.0 tools_4.3.0 knitr_1.42 xfun_0.39 evaluate_0.20