makeSummarizedExperimentFromBam {ORFik} | R Documentation

## Make a count matrix from a library or experiment

### Description

Make a summerizedExperiment / matrix object from bam files

### Usage

    makeSummarizedExperimentFromBam(
      df,
      saveName = NULL,
      longestPerGene = TRUE,
      geneOrTxNames = "tx",
      region = "mrna",
      type = "count"
    )

### Arguments

`df` | an ORFik `experiment`
`saveName` | a character (default NULL), if set save experiment to path given. Always saved as .rds., it is optional to add .rds, it will be added for you if not present. Also used to load existing file with that name.
`longestPerGene` | a logical (default TRUE), if FALSE all transcript isoforms per gene.
`geneOrTxNames` | a character vector (default "tx"), should row names keep trancript names ("tx") or change to gene names ("gene")
`region` | a character vector (default: "mrna"), make raw count matrices of whole mrnas or one of (leaders, cds, trailers). Can also be a `GRangesList`, then it uses this region directly.
`type` | default: "count" (raw counts matrix), alternative is "fpkm", "log2fpkm" or "log10fpkm"

### Details

If txdb or gtf path is added, it is a rangedSummerizedExperiment NOTE: If the file called saveName exists, it will then load file, not remake it!

### Value

a `SummarizedExperiment` object or data.table if "type" is not "count, with rownames as transcript / gene names.

### Examples

    # 1. Pick directory
    dir <- system.file("extdata", "", package = "ORFik")
    # 2. Pick an experiment name
    exper <- "ORFik"
    # 3. Pick .gff/.gtf location
    txdb <- system.file("extdata", "annotations.gtf", package = "ORFik")
    template <- create.experiment(dir = dir, exper, txdb = txdb,
                                  viewTemplate = FALSE)
    template$X5[6] <- "heart" # <- fix non unique row
    # read experiment
    df <- read.experiment(template)

    # makeSummarizedExperimentFromBam(df)
    # Only cds (coding sequences):
    # makeSummarizedExperimentFromBam(df, region = "cds")
    # FPKM instead of raw counts on whole mrna regions
    # makeSummarizedExperimentFromBam(df, type = "fpkm")

[Package ORFik version 1.6.9 Index]