IsomirDataSeqFromRawData {isomiRs} | R Documentation

## 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)

[Package isomiRs version 1.18.1 Index]