## ------------------------------------------------------------------------
dir <- system.file("extdata/salmon_dm", package="tximportData")
# here gzipped, normally these are not
files <- file.path(dir, "SRR1197474_cdna", "quant.sf.gz") 
file.exists(files)
coldata <- data.frame(files, names="SRR1197474", condition="A", stringsAsFactors=FALSE)
coldata

## ----eval=FALSE----------------------------------------------------------
#  library(tximeta)
#  se <- tximeta(coldata)

## ------------------------------------------------------------------------
dir <- system.file("extdata", package="tximeta")
indexDir <- file.path(dir, "Drosophila_melanogaster.BDGP6.cdna.v92_salmon_0.10.2")
fastaFTP <- "ftp://ftp.ensembl.org/pub/release-92/fasta/drosophila_melanogaster/cdna/Drosophila_melanogaster.BDGP6.cdna.all.fa.gz"
dir2 <- system.file("extdata/salmon_dm", package="tximportData")
gtfPath <- file.path(dir2,"Drosophila_melanogaster.BDGP6.92.gtf.gz")
suppressPackageStartupMessages(library(tximeta))
makeLinkedTxome(indexDir=indexDir,
                source="Ensembl",
                organism="Drosophila melanogaster",
                release="92",
                genome="BDGP6",
                fasta=fastaFTP,
                gtf=gtfPath,
                write=FALSE)

## ------------------------------------------------------------------------
library(tximeta)
se <- tximeta(coldata)

## ------------------------------------------------------------------------
suppressPackageStartupMessages(library(SummarizedExperiment))
colData(se)

## ------------------------------------------------------------------------
assayNames(se)

## ------------------------------------------------------------------------
rowRanges(se)

## ------------------------------------------------------------------------
seqinfo(se)

## ------------------------------------------------------------------------
gse <- summarizeToGene(se)
rowRanges(gse)

## ------------------------------------------------------------------------
library(org.Dm.eg.db)
gse <- addIds(gse, "REFSEQ", gene=TRUE)
mcols(gse)

## ------------------------------------------------------------------------
suppressPackageStartupMessages(library(DESeq2))
# here there is a single sample so we use ~1.
# expect a warning that there is only a single sample...
suppressWarnings({dds <- DESeqDataSet(gse, ~1)})
dds <- estimateSizeFactors(dds)
# ... and so on

## ------------------------------------------------------------------------
suppressPackageStartupMessages(library(edgeR))
cts <- assays(gse)[["counts"]]
normMat <- assays(gse)[["length"]]
normMat <- normMat / exp(rowMeans(log(normMat)))
o <- log(calcNormFactors(cts/normMat)) + log(colSums(cts/normMat))
y <- DGEList(cts)
y <- scaleOffset(y, t(t(log(normMat)) + o))
# ... see edgeR User's Guide for further steps

## ------------------------------------------------------------------------
names(metadata(se))
str(metadata(se)[["quantInfo"]])
str(metadata(se)[["txomeInfo"]])
str(metadata(se)[["tximetaInfo"]])
str(metadata(se)[["txdbInfo"]])

## ------------------------------------------------------------------------
dir <- system.file("extdata/salmon_dm/SRR1197474", package="tximportData")
file <- file.path(dir, "quant.sf.gz")
file.exists(file)
coldata <- data.frame(files=file, names="SRR1197474", sample="1",
                      stringsAsFactors=FALSE)

## ------------------------------------------------------------------------
se <- tximeta(coldata)

## ------------------------------------------------------------------------
dir <- system.file("extdata", package="tximeta")
indexDir <- file.path(dir, "Drosophila_melanogaster.BDGP6.v92_salmon_0.10.2")

## ------------------------------------------------------------------------
fastaFTP <- c("ftp://ftp.ensembl.org/pub/release-92/fasta/drosophila_melanogaster/cdna/Drosophila_melanogaster.BDGP6.cdna.all.fa.gz",
              "ftp://ftp.ensembl.org/pub/release-92/fasta/drosophila_melanogaster/ncrna/Drosophila_melanogaster.BDGP6.ncrna.fa.gz")
#gtfFTP <- "ftp://ftp.ensembl.org/pub/release-92/gtf/drosophila_melanogaster/Drosophila_melanogaster.BDGP6.92.gtf.gz"

## ------------------------------------------------------------------------
dir2 <- system.file("extdata/salmon_dm", package="tximportData")
gtfPath <- file.path(dir2,"Drosophila_melanogaster.BDGP6.92.gtf.gz")

## ------------------------------------------------------------------------
tmp <- tempdir()
jsonFile <- file.path(tmp, paste0(basename(indexDir), ".json"))
makeLinkedTxome(indexDir=indexDir,
                source="Ensembl", organism="Drosophila melanogaster",
                release="92", genome="BDGP6",
                fasta=fastaFTP, gtf=gtfPath,
                jsonFile=jsonFile)

## ------------------------------------------------------------------------
se <- tximeta(coldata)

## ------------------------------------------------------------------------
rowRanges(se)
seqinfo(se)

## ------------------------------------------------------------------------
library(BiocFileCache)
if (interactive()) {
  bfcloc <- getTximetaBFC()
} else {
  bfcloc <- tempdir()
}
bfc <- BiocFileCache(bfcloc)
bfcinfo(bfc)
bfcremove(bfc, bfcquery(bfc, "linkedTxomeTbl")$rid)
bfcinfo(bfc)

## ------------------------------------------------------------------------
jsonFile <- file.path(tmp, paste0(basename(indexDir), ".json"))
loadLinkedTxome(jsonFile)

## ------------------------------------------------------------------------
se <- tximeta(coldata)

## ------------------------------------------------------------------------
if (interactive()) {
  bfcloc <- getTximetaBFC()
} else {
  bfcloc <- tempdir()
}
bfc <- BiocFileCache(bfcloc)
bfcinfo(bfc)
bfcremove(bfc, bfcquery(bfc, "linkedTxomeTbl")$rid)
bfcinfo(bfc)

## ------------------------------------------------------------------------
library(devtools)
session_info()