inferSpecies {sesame} | R Documentation |
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,
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 )
sdf |
a |
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. |
a list of auc, pvalue, species (NCBI official species names) and taxid.
if (FALSE) { ## remove this, testing doesn't allow large file caching sdf = sesameDataGet("MM285.1.SigDF") inferSpecies(sdf) }