calcInformation: Compute shannon information based on position and treatment
In gglogo: Geom for Logo Sequence Plots

Description Usage Arguments Value Examples

Compute shannon information based on position and treatment

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

`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.

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

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)