## ----echo=FALSE---------------------------------------------------------------
library(knitr)
opts_chunk$set(tidy=TRUE,message=FALSE)

## -----------------------------------------------------------------------------
library(tximportData)
dir <- system.file("extdata", package="tximportData")
list.files(dir)

## -----------------------------------------------------------------------------
samples <- read.table(file.path(dir,"samples.txt"), header=TRUE)
samples
files <- file.path(dir, "salmon", samples$run, "quant.sf.gz")
names(files) <- paste0("sample",1:6)
all(file.exists(files))

## -----------------------------------------------------------------------------
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
k <- keys(txdb, keytype="TXNAME")
tx2gene <- select(txdb, k, "GENEID", "TXNAME")

## -----------------------------------------------------------------------------
library(readr)
tx2gene <- read_csv(file.path(dir, "tx2gene.gencode.v27.csv"))
head(tx2gene)

## -----------------------------------------------------------------------------
library(tximport)
txi <- tximport(files, type="salmon", tx2gene=tx2gene)
names(txi)
head(txi$counts)

## -----------------------------------------------------------------------------
txi.tx <- tximport(files, type="salmon", txOut=TRUE)

## -----------------------------------------------------------------------------
txi.sum <- summarizeToGene(txi.tx, tx2gene)
all.equal(txi$counts, txi.sum$counts)

## -----------------------------------------------------------------------------
files <- file.path(dir,"salmon", samples$run, "quant.sf.gz")
names(files) <- paste0("sample",1:6)
txi.salmon <- tximport(files, type="salmon", tx2gene=tx2gene)
head(txi.salmon$counts)

## -----------------------------------------------------------------------------
tx2knownGene <- read_csv(file.path(dir, "tx2gene.csv"))
files <- file.path(dir,"sailfish", samples$run, "quant.sf")
names(files) <- paste0("sample",1:6)
txi.sailfish <- tximport(files, type="sailfish", tx2gene=tx2knownGene)
head(txi.sailfish$counts)

## ----eval=FALSE---------------------------------------------------------------
# txi <- tximport("quant.sf", type="none", txOut=TRUE,
#                 txIdCol="Name", abundanceCol="TPM",
#                 countsCol="NumReads", lengthCol="Length",
#                 importer=function(x) read_tsv(x, skip=8))

## -----------------------------------------------------------------------------
files <- file.path(dir,"salmon_gibbs", samples$run, "quant.sf.gz")
names(files) <- paste0("sample",1:6)
txi.inf.rep <- tximport(files, type="salmon", txOut=TRUE)
names(txi.inf.rep)
names(txi.inf.rep$infReps)
dim(txi.inf.rep$infReps$sample1)

## -----------------------------------------------------------------------------
files <- file.path(dir, "kallisto_boot", samples$run, "abundance.h5")
names(files) <- paste0("sample",1:6)
txi.kallisto <- tximport(files, type="kallisto", txOut=TRUE)
head(txi.kallisto$counts)

## -----------------------------------------------------------------------------
names(txi.kallisto)
names(txi.kallisto$infReps)
dim(txi.kallisto$infReps$sample1)

## -----------------------------------------------------------------------------
files <- file.path(dir, "kallisto", samples$run, "abundance.tsv.gz")
names(files) <- paste0("sample",1:6)
txi.kallisto.tsv <- tximport(files, type="kallisto", tx2gene=tx2gene,
                             ignoreAfterBar=TRUE)
head(txi.kallisto.tsv$counts)

## -----------------------------------------------------------------------------
files <- file.path(dir,"rsem", samples$run, paste0(samples$run, ".genes.results.gz"))
names(files) <- paste0("sample",1:6)
txi.rsem <- tximport(files, type="rsem", txIn=FALSE, txOut=FALSE)
head(txi.rsem$counts)

## -----------------------------------------------------------------------------
files <- file.path(dir,"rsem", samples$run, paste0(samples$run, ".isoforms.results.gz"))
names(files) <- paste0("sample",1:6)
txi.rsem <- tximport(files, type="rsem", txIn=TRUE, txOut=TRUE)
head(txi.rsem$counts)

## ----eval=FALSE---------------------------------------------------------------
# tmp <- read_tsv(files[1])
# tx2gene <- tmp[,c("t_name","gene_name")]
# txi <- tximport(files, type="stringtie", tx2gene=tx2gene)

## ----eval=FALSE---------------------------------------------------------------
# files <- "path/to/alevin/quants_mat.gz"
# txi <- tximport(files, type="alevin")

## -----------------------------------------------------------------------------
sgnex_file <- "sgnex_h9"
files <- file.path(dir,"oarfish", 
  paste0(sgnex_file, "_rep", 2:4, ".quant.gz")
) 
names(files) <- paste0("sgnex-rep",2:4)
txi.oar <- tximport(files, type="oarfish", txOut=TRUE)

## ----results="hide", messages=FALSE-------------------------------------------
library(DESeq2)

## -----------------------------------------------------------------------------
sampleTable <- data.frame(condition=factor(rep(c("A","B"),each=3)))
rownames(sampleTable) <- colnames(txi$counts)

## -----------------------------------------------------------------------------
dds <- DESeqDataSetFromTximport(txi, sampleTable, ~ condition)
# dds is now ready for DESeq()
# see DESeq2 vignette

## ----results="hide", messages=FALSE-------------------------------------------
library(edgeR)
dge <- DGEListFromTximport(txi)

## ----results="hide", messages=FALSE-------------------------------------------
library(edgeR)
dge.tx <- DGEListFromTximport(txi.tx, divide=TRUE)

## -----------------------------------------------------------------------------
sessionInfo()