dagLogo-package {dagLogo}R Documentation

Visualize significant conserved amino acid sequence pattern in groups based on probability theory

Description

dagLogo provides differential analysis of grouped/ungrouped amino acid usage between an input set of aligned peptide sequences and a background set of aligned peptide sequences which can be generated in different ways. Results of Fisher's exact test and/or Z-test are visualized using a heatmap or DAG Logo.

Details

DAG: Differential Amino acid Group

There are several differences between dagLogo from iceLogo:

1. The sequence patterns can be grouped by charge, chemistry, hydrophobicity and etc.

2. dagLogo accepts different length of unaligned amino acid sequences.

3. dagLogo not only can build random, regional (called restricted in dagLogo) and terminal (called anchored) background model from the whole proteome, but also it can generate the background set using the aa sequences of the input protein excluding the input regions/sequences or the complementary set of the input set.

Author(s)

Jianhong Ou, Haibo Liu, Julie Lihua Zhu

Maintainer: Jianhong Ou <jianhong.ou@duke.edu>

Examples

  data("seq.example")
  data("proteome.example")
  bg <- buildBackgroundModel(seq.example, proteome=proteome.example, numSubsamples=10L)
  t <- testDAU(seq.example, bg)
  dagLogo(t)

[Package dagLogo version 1.22.0 Index]