heatMapRegion {ORFik} | R Documentation

## Create coverage heatmaps of specified region

### Description

Simplified input space for easier abstraction of coverage heatmaps
Pick your transcript region and plot directly
Input CAGE file if you use TSS and want improved 5' annotation.

### Usage

    heatMapRegion(
      df,
      region = "TIS",
      outdir = "default",
      scores = c("transcriptNormalized", "sum"),
      type = "ofst",
      cage = NULL,
      plot.ext = ".pdf",
      acceptedLengths = 21:75,
      upstream = c(50, 30),
      downstream = c(29, 69),
      shifting = c("5prime", "3prime"),
      longestPerGene = FALSE,
      BPPARAM = BiocParallel::SerialParam()
    )

### Arguments

`df` | an ORFik `experiment`
`region` | a character, default "TIS". The centering point for the heatmap (what is position 0, beween -50 and 50 etc), can be any combination of the set: c("TSS", "TIS", "TTS", "TES"), which are: - Transcription start site (5' end of mrna) - Translation initation site (5' end of CDS) - Translation termination site (5' end of 3' UTRs) - Transcription end site (3' end of 3' UTRs)
`outdir` | a character path, default: "default", saves to: `paste0(dirname(df$filepath[1]), "/QC_STATS/heatmaps/")`, a created folder within the ORFik experiment data folder for plots. Change if you want custom location.
`scores` | character vector, default `c("transcriptNormalized", "sum")`, either of zscore, transcriptNormalized, sum, mean, median, .. see ?coverageScorings for info and more alternatives.
`type` | character, default: "ofst". Type of library: either "default", usually bam format (the one you gave to experiment), "pshifted" pshifted reads, "ofst", "bed", "bedo" optimized bed, or "wig"
`cage` | a character path to library file or a `GRanges`, `GAlignments` preloaded file of CAGE data. Only used if "TSS" is defined as region, to redefine 5' leaders.
`plot.ext` | a character, default ".pdf", alternative ".png"
`acceptedLengths` | an integer vector (NULL), the read lengths accepted. Default NULL, means all lengths accepted.
`upstream` | 1 or 2 integers, default c(50, 30), how long upstream from 0 should window extend (first index is 5' end extension, second is 3' end extension). If only 1 shifting, only 1 value should be given, if two are given will use first.
`downstream` | 1 or 2 integers, default c(29, 69), how long upstream from 0 should window extend (first index is 5' end extension, second is 3' end extension). If only 1 shifting, only 1 value should be given, if two are given will use first.
`shifting` | a character, default c("5prime", "3prime"), can also be NULL (no shifting of reads). If NULL, will use first index of 'upstream' and 'downstream' argument.
`longestPerGene` | logical (TRUE), return only longest valid transcript per gene. NOTE: This is by priority longest cds isoform, if equal then pick longest total transcript. So if transcript is shorter but cds is longer, it will still be the one returned.
`BPPARAM` | a core param, default: single thread: `BiocParallel::SerialParam()`. Set to `BiocParallel::bpparam()` to use multicore. Be aware, this uses a lot of extra ram (40GB+) for larger human samples!

### Value

invisible(NULL), plots are saved

### See Also

Other heatmaps: `coverageHeatMap()`, `heatMapL()`, `heatMap_single()`

### Examples

    # Toy example, will not give logical output, but shows how it works
    df <- ORFik.template.experiment()[3,] # Only third library
    #heatMapRegion(df, "TIS", outdir = "default")
    #
    # Do also TSS, add cage for specific TSS
    # heatMapRegion(df, c("TSS", "TIS"), cage = "path/to/cage.bed")

    # Do on pshifted reads instead of original files
    remove.experiments(df) # Remove loaded experiment first
    # heatMapRegion(df, "TIS", type = "pshifted")

[Package ORFik version 1.14.7 Index]