IsomirDataSeqFromRawData: Loads miRNA annotation from seqbuster tool or pre-processed...

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

Loads miRNA annotation from seqbuster tool or pre-processed data.

Description

Process raw data like tables to speed up filtering steps.

Usage

IsomirDataSeqFromRawData(
  rawdata,
  coldata,
  design = ~1L,
  pct = 0.1,
  n_snv = 1,
  whitelist = NULL,
  ...
)

Arguments

rawdata	data.frame stored in metadata slot of IsomirDataSeq object.
coldata	data frame containing groups for each sample
design	a formula to pass to DESeq2::DESeqDataSet
pct	numeric used to remove isomiRs with an importance lower than this value. Importance is calculated by dividing the isomiR count by the total counts of the miRNA to which it maps.
n_snv	numeric used to remove isomiRs with more than this number of single nucleotide variants (indels are counted here).
whitelist	character vector with sequences to keep even if the filtering step would have removed them. They have to match the seq column in the table.
...	arguments provided to SummarizedExperiment. including rowData.

Value

IsomirDataSeq class object.

Examples

path <- system.file("extra", package="isomiRs")
fn_list <- list.files(path, pattern="mirna", full.names = TRUE)
de <- data.frame(row.names=c("f1" , "f2"),
                 condition = c("newborn", "newborn"))
ids <- IsomirDataSeqFromFiles(fn_list, coldata=de)

head(counts(ids))
IsomirDataSeqFromRawData(metadata(ids)[["rawData"]], de)

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