transcriptWindow {ORFik}R Documentation

Make 100 bases size meta window for all libraries in experiment

Description

Gives you binned meta coverage plots, either saved seperatly or all in one.

Usage

transcriptWindow(
  leaders,
  cds,
  trailers,
  df,
  outdir = NULL,
  scores = c("sum", "zscore"),
  allTogether = TRUE,
  colors = rep("skyblue4", nrow(df)),
  title = "Coverage metaplot",
  windowSize = min(100, min(widthPerGroup(leaders, FALSE)), min(widthPerGroup(cds,
    FALSE)), min(widthPerGroup(trailers, FALSE))),
  returnPlot = is.null(outdir),
  dfr = NULL,
  idName = "",
  format = ".png"
)

Arguments

leaders

a GRangesList of leaders (5' UTRs)

cds

a GRangesList of coding sequences

trailers

a GRangesList of trailers (3' UTRs)

df

an ORFik experiment

outdir

directory to save to (default: NULL, no saving)

scores

scoring function (default: c("sum", "zscore")), see ?coverageScorings for possible scores.

allTogether

plot all coverage plots in 1 output? (defualt: TRUE)

colors

Which colors to use, default (skyblue4)

title

title of ggplot

windowSize

size of binned windows, default: 100

returnPlot

return plot from function, default is.null(outdir), so TRUE if outdir is not defined.

dfr

an ORFik experiment of RNA-seq to normalize against. Will add RNA normalized to plot name if this is done.

idName

A character ID to add to saved name of plot, if you make several plots in the same folder, and same experiment, like splitting transcripts in two groups like targets / nontargets etc. (default: "")

format

default (".png"), do ".pdf" if you want as pdf

Value

NULL, or ggplot object if returnPlot is TRUE

Examples

# Make ORFik experiment
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)
loadRegions(df) # Load leader, cds and trailers as GRangesList
#transcriptWindow(leaders, cds, trailers, df, outdir = "directory_to_save")
[Package ORFik version 1.7.21 Index]