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/quants
directory. The quant.sf files have been gzipped to preserve space,
so they are stored as quant.sf.gz. Salmon was run with 20 Gibbs
inferential replicates for each sample. To reduce the size of the
package, the inferential replicates (aux_info/bootstrap) and the
aux_info/ambig_info.tsv files are no longer included in
inst/extdata/quants (as of version 1.29.1). The full Salmon output,
including the inferential replicates, is archived on Zenodo:
doi: 10.5281/zenodo.22982581.
The inferential replicates for a subset of genes are provided in the
macro_txp_se object (see below).
The file inst/extdata/gencode.v29.annotation.slim.gtf.gz is a
reduced version of the Gencode v29 GTF file, containing only the
gene and transcript features, with a subset of the attributes
(gene_id, transcript_id, gene_type, gene_name,
transcript_type, transcript_name). It can be used to build
transcript and gene ranges, but not exon ranges. It was created with
the script inst/scripts/makeSlimGTF.sh.
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").
Additionally, the package contains a transcript-level
SummarizedExperiment, macro_txp_se, including the 20 inferential
replicates, for all transcripts of a random subset of 2000 expressed
genes plus the GBP gene family, and a transcript-to-gene table,
macro_tx2gene. These were created with the script in
inst/scripts/makeSumExp.R and are used in the fishpond vignette.
See ?macro_txp_se and ?macro_tx2gene for details.
Thanks to the study authors for posting their data publicly and clearly labelling their data.
sessionInfo()
## R version 4.6.1 (2026-06-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.5 LTS
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## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.24-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0 LAPACK version 3.12.0
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## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
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## time zone: America/New_York
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## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
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## loaded via a namespace (and not attached):
## [1] compiler_4.6.1 cli_3.6.6 tools_4.6.1 otel_0.2.0 knitr_1.52
## [6] xfun_0.61 rlang_1.3.0 evaluate_1.0.5