testDAU {dagLogo} | R Documentation |
Test differential usage of amino acids with or without grouping in experimental sets and background sets.
testDAU(dagPeptides, dagBackground, groupingScheme = ls(envir = cachedEnv), bgNoise = NA)
dagPeptides |
An object of Class |
dagBackground |
An object of 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. |
An object of Class testDAUresults-class
.
Jianhong Ou, Haibo Liu
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 t0 <- testDAU(seq, dagBackground = bg_ztest) ## 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")