View source: R/SignatureGATAIGeneRemoval.R
SignatureGATAIGeneRemoval | R Documentation |
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).
SignatureGATAIGeneRemoval(
ExpressionSet,
plot_type = "separate",
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",
...
)
ExpressionSet |
a standard PhyloExpressionSet, DivergenceExpressionSet or PolymorphismsExpressionSet object. |
plot_type |
a string defining specifying the type of visualization for the results. If:
|
measure |
type of transcriptome index that shall be computed. E.g.
|
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:
|
modules |
a list storing three elements for the
|
permutations |
a numeric value specifying the number of permutations to be performed for the |
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 |
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 |
y.ticks |
number of ticks on the y-axis. Default is |
n_random_removal |
number of randomly removed genes for the third plot. Default is |
Filipa Martins Costa
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