gglogo (version 0.1.5)

calcInformation: Compute shannon information based on position and treatment

Description

Compute shannon information based on position and treatment

Usage

calcInformation(
  dframe,
  pos,
  elems,
  trt = NULL,
  weight = NULL,
  k = 4,
  method = "shannon"
)

Arguments

dframe

data frame of peptide (or any other) sequences and some treatment factors

pos

variable containing position

elems

variable containing elements

trt

(vector of) character string(s) of treatment information

weight

variable containing number of times each sequence is observed, defaults to 1 in case no weight is given

k

alphabet size: 4 for DNA/RNA sequences, 21 for standard amino acids

method

either "shannon" or "frequency" for Shannon information or relative frequency of element by position.

Value

extended data frame with additional information of shannon info in bits and each elements contribution to the total information

Examples

# NOT RUN {
data(sequences)
dm2 <- splitSequence(sequences, peptide)
dm3 <- calcInformation(dm2, pos = position, elems = element, trt = class, k = 21)
# precursor to a logo plot:
library(ggplot2)
# library(biovizBase)

# }