inferSpecies {sesame}R Documentation

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,
  df_as = NULL,
  topN = 3000,
  threshold.pos = 0.01,
  threshold.neg = 0.1,
  ret.max = TRUE,
  balance = TRUE,
  threshold.sucess.rate = 0.8
)

Arguments

sdf

a SigSet

df_as

a data.frame of alignment score for each probe.

topN

Top n positive and negative probes used to infer species.

threshold.pos

pvalue < threshold.pos are considered positive (default: 0.01).

threshold.neg

pvalue > threshold.neg are considered negative (default: 0.2).

ret.max

whether to return the species with maximal AUC.

balance

whether to balance the postive and negative probe number (default: TRUE).

threshold.sucess.rate

threshold of success rate to determine mouse species.

Value

a list of auc, pvalue, species (NCBI official species names) and taxid.

Examples

if (FALSE) { ## remove this, testing doesn't allow large file caching
  sdf = sesameDataGet("MM285.1.SigDF")
  inferSpecies(sdf)
}

[Package sesame version 1.12.0 Index]