IsomirDataSeqFromMirtop: Import 'mirtop' output into 'IsomirDataSeq'

In lpantano/isomiRs: Analyze isomiRs and miRNAs from small RNA-seq

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 March 14, 2024, 7:19 a.m.