parse_salmon_flenfile: Parse Salmon fragment length file

In jmw86069/platjam: Platform Jam, biological platform importers.

Parse Salmon fragment length file

Description

Parse Salmon fragment length file

Usage

parse_salmon_flenfile(
  x,
  k = 7,
  do_plot = FALSE,
  retcolors = c("red", "gold", "dodgerblue", "grey"),
  probs = c(0.25, 0.75),
  ...
)

Arguments

x	character path to file usually named "flenDist.txt".
k	numeric used with caTools::runmean() to define the width for smoothing a running mean, helpful to de-noise the fragment length profile.
do_plot	logical indicating whether to plot the data and resulting values.
retcolors	character vector with three colors used when do_plot=TRUE: mean, median, mode.
...	additional arguments are passed to plot() when do_plot=TRUE.

Value

numeric vector with summary values:

• mean: the weighted mean across the fragment length distribution

• median: the position with 50% cumulative density at or below

• mode: the position with the highest density

• each value in probs representing percentiles

value representing the weighted mean across the fragment lengths reported, typically values from 1 to 1000.

See Also

Other jam nextgen sequence functions: get_salmon_meta(), get_salmon_root(), save_salmon_qc_xlsx()

jmw86069/platjam documentation built on Sept. 26, 2024, 3:31 p.m.