calcInformation: Compute shannon information based on position and treatment

In heike/gglogo: Geom for Logo Sequence Plots

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 frequency and (Shanon) bits. The results for the requested method are found in variable 'info'.

Examples

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)

heike/gglogo documentation built on Feb. 3, 2024, 1:45 p.m.