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Removed genes after GATAI gene removal and plots of evolutionary signatures across transcriptomes before, after GATAI gene removal and with randomly removed genes

Source: R/SignatureGATAIGeneRemoval.R
SignatureGATAIGeneRemoval.Rd

Main function to return the removed genes after GATAI gene removal and plots transcriptome indices pattern before, after GATAI gene removal and by removing random genes (by default same number as GATAI removed).

Usage

SignatureGATAIGeneRemoval(
  ExpressionSet,
  measure = "TAI",
  TestStatistic = "FlatLineTest",
  modules = NULL,
  permutations = 1000,
  lillie.test = FALSE,
  p.value = TRUE,
  shaded.area = FALSE,
  custom.perm.matrix = NULL,
  xlab = "Ontogeny",
  ylab = "Transcriptome Index",
  main = "",
  lwd = 4,
  alpha = 0.1,
  y.ticks = 10,
  n_random_removal = "gatai",
  ...
)

Arguments

ExpressionSet

a standard PhyloExpressionSet, DivergenceExpressionSet or PolymorphismsExpressionSet object.

measure

type of transcriptome index that shall be computed. E.g.

  • measure = "TAI" (Transcriptome Age Index)

  • measure = "TDI" (Transcriptome Divergence Index)

  • measure = "TPI" (Transcriptome Polymorphism Index)

TestStatistic

a string defining the type of test statistics to be used to quantify the statistical significance the present phylotranscriptomics pattern. Possible values can be:

  • TestStatistic = "FlatLineTest" : Statistical test for the deviation from a flat line

  • TestStatistic = "ReductiveHourglassTest" : Statistical test for the existence of a hourglass shape (high-low-high pattern)

  • TestStatistic = "EarlyConservationTest" : Statistical test for the existence of a early conservation pattern (low-high-high pattern)

  • TestStatistic = "LateConservationTest" : Statistical test for the existence of a late conservation pattern (high-high-low pattern)

  • TestStatistic = "ReverseHourglassTest" : Statistical test for the existence of a reverse hourglass pattern (low-high-low pattern)

modules

a list storing three elements for the ReductiveHourglassTest, EarlyConservationTest, LateConservationTest, or ReverseHourglassTest: early, mid, and late. Each element expects a numeric vector specifying the developmental stages or experiments that correspond to each module. For example:

  • module = list(early = 1:2, mid = 3:5, late = 6:7) divides a dataset storing seven developmental stages into 3 modules.

permutations

a numeric value specifying the number of permutations to be performed for the FlatLineTest, EarlyConservationTest, LateConservationTest, ReductiveHourglassTest or ReverseHourglassTest.

lillie.test

a boolean value specifying whether the Lilliefors Kolmogorov-Smirnov Test shall be performed.

p.value

a boolean value specifying whether the p-value of the test statistic shall be printed as a subtitle.

shaded.area

a boolean value specifying whether a shaded area shall be drawn for the developmental stages defined to be the presumptive phylotypic period.

custom.perm.matrix

a custom bootMatrix (permutation matrix) to perform the underlying test statistic visualized by PlotSignature. Default is custom.perm.matrix = NULL.

xlab

label of x-axis.

ylab

label of y-axis.

main

figure title.

lwd

line width.

alpha

transparency of the shaded area (between [0,1]). Default is alpha = 0.1.

y.ticks

number of ticks on the y-axis. Default is ticks = 10.

n_random_removal

number of randomly removed genes for the third plot. Default is gatai (same number of genes removed by GATAI).

...

parameters passed on to GATAI.

Author

Filipa Martins Costa and Hajk-Georg Drost