IsomirDataSeqFromMirtop: Import 'mirtop' output into 'IsomirDataSeq'
In lpantano/isomiRs: Analyze isomiRs and miRNAs from small RNA-seq

IsomirDataSeqFromMirtop

R Documentation

Import `mirtop` output into `IsomirDataSeq`

Description

The tabular output of mirtop is compatible with IsomirDataSeq. This function allows to import the data and filter low confidence isomiRs for downstream analysis.

Usage

IsomirDataSeqFromMirtop(mirtop, coldata, ...)

Arguments

`mirtop`	data.frame with the output of `⁠mirtop export⁠`
`coldata`	data.frame with the metadata of the samples
`...`	It supports the same parameters as in IsomirDataSeqFromRawData.

Details

The output is generated with ⁠mirtop export --format isomir⁠.

Value

IsomirDataSeq class object.

Examples

library(readr)
path <- system.file("extra", "mirtop", package="isomiRs")
fn <- list.files(path, full.names = TRUE)
de <- data.frame(row.names=c("sample1" , "sample2"),
                 condition = c("cc", "cc"))
# mirtop export --format isomir ....
IsomirDataSeqFromMirtop(read_tsv(fn), de)

lpantano/isomiRs documentation built on Aug. 26, 2024, 3:34 a.m.