working on new chapter

Author: mikelove

isoform-assignment.Rmd

@@ -0,0 +1,35 @@
+# Isoform assignment
+
+Objective: explore consequences of how features are located when data
+is summarized at gene level.
+
+The *macrophage* package provides Salmon quantification files for a
+set of 24 RNA-seq samples from @Alasoo2018, "Shared genetic effects
+on chromatin and gene expression indicate a role for enhancer priming in
+immune response". Data for six female human donors is available in the
+package, with gene expression at baseline, after IFN-gamma stimulation,
+after exposure to *Salmonella*, and after a combination of the two
+treatments.
+
+```{r message=FALSE}
+library(macrophage)
+library(dplyr)
+library(tximeta)
+dir <- system.file("extdata", package="macrophage")
+coldata <- read.csv(file.path(dir, "coldata.csv")) %>%
+  mutate(files = file.path(dir, "quants", names, "quant.sf.gz"),
+         condition = factor(condition_name),
+         condition = relevel(condition, "naive")) %>%
+  select(files, names=sample_id, condition, line_id)
+se <- tximeta(coldata, dropInfReps=TRUE)
+```
+
+```{r message=FALSE}
+library(SummarizedExperiment)
+rowRanges(se)
+seqinfo(se)
+```
+
+```{r}
+gse <- summarizeToGene(se)
+```

references.bib

@@ -225,3 +225,28 @@ @article{rainer2019
     url = {https://doi.org/10.1093/bioinformatics/btz031},
     eprint = {https://academic.oup.com/bioinformatics/article-pdf/35/17/3151/29592004/btz031.pdf},
 }
+
+@Article{Alasoo2018,
+author={Alasoo, Kaur
+and Rodrigues, Julia
+and Mukhopadhyay, Subhankar
+and Knights, Andrew J.
+and Mann, Alice L.
+and Kundu, Kousik
+and Hale, Christine
+and Dougan, Gordon
+and Gaffney, Daniel J.
+and Consortium, H. I. P. S. C. I.},
+title={Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response},
+journal={Nature Genetics},
+year={2018},
+month={Mar},
+day={01},
+volume={50},
+number={3},
+pages={424-431},
+issn={1546-1718},
+doi={10.1038/s41588-018-0046-7},
+url={https://doi.org/10.1038/s41588-018-0046-7}
+}
+