inferSpecies: Infer Species

In zwdzwd/sesame: SEnsible Step-wise Analysis of DNA MEthylation BeadChips

Infer Species

Description

We infer species based on probes pvalues and alignment score. AUC was calculated for each specie, y_true is 1 or 0 for pval < threshold.pos or pval > threshold.neg, respeceively,

Usage

inferSpecies(
  sdf,
  topN = 1000,
  threshold.pos = 0.01,
  threshold.neg = 0.1,
  return.auc = FALSE,
  return.species = FALSE,
  verbose = FALSE
)

Arguments

sdf	a SigDF
topN	Top n positive and negative probes used to infer species. increase this number can sometimes improve accuracy (DEFAULT: 1000)
threshold.pos	pvalue < threshold.pos are considered positive (default: 0.01).
threshold.neg	pvalue > threshold.neg are considered negative (default: 0.2).
return.auc	return AUC calculated, override return.species
return.species	return a string to represent species
verbose	print more messaeges

Value

a SigDF

Examples

sdf <- sesameDataGet("MM285.1.SigDF")
sdf <- inferSpecies(sdf)

## all available species
all_species <- names(sesameDataGet(sprintf(
  "%s.addressSpecies", sdfPlatform(sdf)))$species)

zwdzwd/sesame documentation built on Nov. 11, 2024, 9:33 a.m.