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What does tximport do?
The tximport package has a single function for importing transcript-level estimates. The type argument is used to specify what software was used for estimation. A simple list with matrices, “abundance” , “counts” , and “length” , is returned, where the transcript level information is summarized to the gene-level.
What is abundance tximport?
The tximport package has a single function for importing transcript-level estimates. Typically, abundance is provided by the quantification tools as TPM (transcripts-per-million), while the counts are estimated counts (possibly fractional), and the “length” matrix contains the effective gene lengths.
What is a TxDb object?
The GenomicFeatures package uses TxDb objects to store transcript metadata. All TxDb objects are backed by a SQLite database that manages genomic locations and the relationships between pre-processed mRNA transcripts, exons, protein coding sequences, and their related gene identifiers.
What is CPM in RNA-seq?
CPM. The simplest RNA-seq feature expression unit reports normalized counts, or the number of reads that align to a particular feature after correcting for sequencing depth and transcriptome composition bias. This unit is known as counts per million reads mapped (CPM).
How can I import salmon results into deseq2?
Using the tximport package, you can import salmon’s transcript-level quantifications and optionally aggregate them to the gene level for gene-level differential expression analysis. You can read more about how to import salmon’s results into DESeq2 by reading the tximport section of the excellent DESeq2 vignette .
What kind of transcriptome do you need for salmon?
Obtaining a transcriptome and building an index In order to quantify transcript-level abundances, Salmon requires a target transcriptome. This transcriptome is given to Salmon in the form of a (possibly compressed) multi-FASTA file, with each entry providing the sequence of a transcript 1.
How to import a quant.sf file into tximport?
For example, using the following code chunk (un-evaluated): If inferential replicates (Gibbs or bootstrap samples) are present in expected locations relative to the quant.sf file, tximport will import these as well.
How to import readr files in tximport 1.2?
If tximport detects that readr is installed, then it will use the readr::read_tsv function by default. A change from version 1.2 to 1.4 is that the reader is not specified by the user anymore, but chosen automatically based on the availability of the readr package. Advanced users can still customize the import of files using the importer argument.