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 1.12.9 Index]