testDAU: Differential usage test of amino acids or amino acid groups.

In jianhong/dagLogo: dagLogo: a Bioconductor package for visualizing conserved amino acid sequence pattern in groups based on probability theory

Differential usage test of amino acids or amino acid groups.

Description

Test differential usage of amino acids with or without grouping between experimental sets and background sets.

Usage

testDAU(
  dagPeptides,
  dagBackground,
  groupingScheme = ls(envir = cachedEnv),
  bgNoise = NA,
  method = "none"
)

Arguments

dagPeptides	An object of Class dagPeptides-class.
dagBackground	An object of Class dagBackground-class.
groupingScheme	A character vector of length 1. Available choices are "no","bulkiness_Zimmerman","hydrophobicity_KD", "hydrophobicity_HW", "isoelectric_point_Zimmerman", "contact_potential_Maiorov", "chemistry_property_Mahler", "consensus_similarity_SF", "volume_Bigelow", "structure_alignments_Mirny", "polarity_Grantham", "sequence_alignment_Dayhoff", "bulkiness_Zimmerman_group", "hydrophobicity_KD_group", "hydrophobicity_HW_group", "charge_group", "contact_potential_Maiorov_group", "chemistry_property_Mahler_group", "consensus_similarity_SF_group", "volume_Bigelow_group", "structure_alignments_Mirny_group", "polarity_Grantham_group", "sequence_alignment_Dayhoff_group", "custom" and "custom_group". If "custom" or "custom_group" are used, users must define a grouping scheme using a list containing sublist named as "color", and "symbol" using the function addScheme, with group set as "NULL" or a list with same names as those of color and symbol. No grouping was applied for the first 12 schemes. It is used to color AAs based on similarities or group amino acids into groups of similarities.
bgNoise	A numeric vector of length 1 if not NA. It should be in the interval of (0, 1) when not NA.
method	A character vector of length 1, specifying the method used for p-value adjustment to correct for multiple testing. it can be "holm", "hochberg", "hommel","bonferroni", "BH", "BY", "fdr", or "none". For more details, see p.adjust.methods and p.adjust.

Value

An object of Class testDAUresults-class.

Author(s)

Jianhong Ou, Haibo Liu

Examples

dat <- unlist(read.delim(system.file(
                                   "extdata", "grB.txt", package = "dagLogo"),
                         header = FALSE, as.is = TRUE))
                         
##prepare an object of Proteome Class from a fasta file
proteome <- prepareProteome(fasta = system.file("extdata",
                                                "HUMAN.fasta",
                                                package = "dagLogo"), 
                            species = "Homo sapiens")
##prepare an object of dagPeptides Class
seq <- formatSequence(seq = dat, proteome = proteome, upstreamOffset = 14,
                     downstreamOffset = 15)
bg_fisher <- buildBackgroundModel(seq, background = "wholeProteome",
                                  proteome = proteome, testType = "fisher")
bg_ztest <- buildBackgroundModel(seq, background = "wholeProteome",
                                   proteome = proteome, testType = "ztest")

## no grouping and distinct coloring scheme, adjust p-values using the 
## "BH" method.
t0 <- testDAU(seq, dagBackground = bg_ztest, method = "BY")

## grouped by polarity index (Granthm, 1974)
t1 <- testDAU(dagPeptides = seq, dagBackground = bg_ztest, 
             groupingScheme = "polarity_Grantham_group")
             
## grouped by charge.
t2 <- testDAU(dagPeptides = seq, dagBackground = bg_ztest, 
              groupingScheme = "charge_group")
              
## grouped on the basis of the chemical property of side chains.
t3 <- testDAU(dagPeptides = seq, dagBackground = bg_ztest, 
              groupingScheme = "chemistry_property_Mahler_group")
              
## grouped on the basis of hydrophobicity (Kyte and Doolittle, 1982)
t4 <- testDAU(dagPeptides = seq, dagBackground = bg_ztest, 
              groupingScheme = "hydrophobicity_KD_group") 

jianhong/dagLogo documentation built on Oct. 27, 2023, 2:14 p.m.