getInputSpecies: Return Miranda data for a given species.

In Mercedeh66/mirTarRnaSeq: mirTarRnaSeq

Return Miranda data for a given species.

Description

Reads Miranda file for a given speicies and returns it as a data.frame, thresholded by percent identity. Header options are Score (threshold), Energy-Kcal/Mol(energy), Subject-IdentityPercent(targetIden), Query-IdentityPercent (mirnaIden)

Usage

getInputSpecies(
  selection,
  threshold = 60,
  energy = NULL,
  targetIden = NULL,
  mirnaIden = NULL
)

Arguments

selection	Species (species selection are either for mature miRNA species "Human1","Mouse", "C.elegans", "Epstein_Barr", "Epstein_Barr_Human", "Drosophila","Kaposi_Sarcoma", "KSHV_Human", "Cytomegalovirus","CMV_Human")
threshold	miRanda score threshold default 60
energy	miRanda folding energy threshold default NULL
targetIden	miRanda target identity score default NULL
mirnaIden	miRanda mirna identity score default NULL

Value

data.frame with Miranda data.

Examples

x <- getInputSpecies("Epstein_Barr", threshold = 60) # Default is threshold 60

Mercedeh66/mirTarRnaSeq documentation built on April 14, 2023, 6:49 a.m.