MCUFD_enrich-list-method: MCUFD enrichment testing

In adamd3/codondiffR: Codon usage comparisons across taxa

MCUFD enrichment testing

Description

Compare taxon proportions in the top n hits with those in the full set of taxa.

Usage

## S4 method for signature 'list'
MCUFD_enrich(
  cFres,
  n = NA_real_,
  rank = "Phylum",
  save = FALSE,
  pthresh = NA_real_,
  fname = NA_character_,
  units = "in",
  width = 10,
  height = 7,
  dpi = 600,
  ptype = "heatmap",
  outtab = NULL
)

Arguments

cFres	List of data frames containing MCUFD results.
n	Numeric, the number of top-ranked reference taxa to be plotted per input sequence. Default = 100.
rank	Character, taxonomic rank to be used for categorisation of the CUFD hit sequences. Options are "Domain", "Kingdom", and "Phylum". Default = "Phylum".
save	Logical, should the enrichment plot be saved to file? Default = FALSE.
pthresh	Numeric, adjusted p-value threshold to be used for subsetting the data if plot == TRUE. Default = NA.
fname	Character, name of the output file (used if plot == TRUE).
units	Numeric, units to be used for defining the plot size. Options are "in" (default), "cm", and "mm".
width	Numeric, width of the figure (in units).
height	Numeric, height of the figure (in units).
dpi	Numeric, resolution of the figure (default = 600).
ptype	Character, type of plot to make (if plot == TRUE). Options are "heatmap" (default) and "dotplot".
outtab	Character (optional); name of file to which enrichment test results will be saved. Format is tab-delimited.

Value

A ggplot object.

Examples

   virusSet <- readSeq(example = TRUE)
   virusCF <- codonFreq(virusSet)
   exclCod <- c("ATT", "TGT")
   MCUFD_tmp <- MCUFD(virusCF, exclude = exclCod, norm = TRUE)
   enrich_tmp <- MCUFD_enrich(
       MCUFD_tmp, n = 100, rank = "Phylum", save = FALSE, pthresh = 0.01
   )

adamd3/codondiffR documentation built on Sept. 3, 2022, 2:26 a.m.