https://github.com/mikelove/airway_quants

Salmon quantifications of samples from the Bioconductor 'airway' package
https://github.com/mikelove/airway_quants

Last synced: 24 days ago
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Salmon quantifications of samples from the Bioconductor 'airway' package

• Host: GitHub
• URL: https://github.com/mikelove/airway_quants
• Owner: mikelove
• License: mit
• Created: 2017-07-13T19:58:06.000Z (over 7 years ago)
• Default Branch: master
• Last Pushed: 2017-07-13T20:11:13.000Z (over 7 years ago)
• Last Synced: 2024-05-09T07:53:19.267Z (6 months ago)
• Language: R
• Size: 23.6 MB
• Stars: 1
• Watchers: 2
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.Rmd
  • License: LICENSE

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README

        
# Salmon quants for the 'airway' package

## How to read these into R and make a DESeqDataSet

```{r}

library(readr)

coldata <- read_delim("data/SraRunTable.txt", delim="\t")

coldata$cell <- factor(coldata$cell_line_s)

coldata$dex <- factor(coldata$treatment_s)

coldata$dex

levels(coldata$dex) <- rep(c("trt","untrt"),4)

coldata$dex <- relevel(coldata$dex, "untrt")

```

```{r}

coldata <- coldata[c("Run_s","cell","dex")]

coldata <- coldata[order(coldata$dex, coldata$cell),]

files <- file.path("data/quant",coldata$Run_s,"quant.sf.gz")

names(files) <- coldata$Run_s

```

```{r}

library(tximport)

load("data/tx2gene.rda") # see mikelove/asthma/scripts/asthma.Rmd

txi <- tximport(files, type="salmon", tx2gene=tx2gene)

library(DESeq2)

dds <- DESeqDataSetFromTximport(txi, coldata, ~cell + dex)

```