Description Usage Arguments Details Value See Also
Functions to transform the gene-level statistic values prior to the calculation of the gene set statistics, as used in the transformation
parameter of gsAnalysis
. Most of the functions wrap existing R functions.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | transformation.abs(x)
transformation.square(x)
transformation.localFdr(x,
statistic="pvalue",
cutoff.method="fndr",
pct0=0.75)
transformation.binarize(x, quant)
transformation.rank(x)
transformation.adjust(x, adjMethod = "fdr")
transformation.adjustAndBinarize(x, adjMethod = "fdr", threshold = 0.05)
|
x |
A numeric vector of gene-level statistic values, one per gene. These values are calculated by the previous step (see |
statistic |
Specifies the null model for |
cutoff.method |
Type of cut-off method used in |
pct0 |
Fraction of data used by |
quant |
For |
adjMethod |
The method to use for the adjustment for multiple testing (see |
threshold |
The threshold for differential expression of a gene (defaults to |
Standard transformation functions for gene-level statistics (to be used in an analysis pipeline defined by gsAnalysis
):
transformation.abs
:
Calculates the absolute values of the elements in x
(a wrapper for abs
).
transformation.square
:
Squares all elements in x
.
transformation.localFdr
:
Calculates the local fdr for the elements in x
. This is a wrapper for fdrtool
.
transformation.binarize
:
Binarizes the values in x
by using the quant
quantile as a threshold.
transformation.rank
:
Ranks the values in x
and returns the rank vector.
transformation.adjust
:
Adjusts for multiple testing according to the adjustment method specified in adjMethod
.
transformation.adjustAndBinarize
:
Adjusts for multiple testing according to the adjustment method specified in adjMethod
and binarizes the resulting p-values according to threshold
(values smaller than the threshold become 1 others 0).
All functions return a vector of transformed values having the same length as x
.
geneSetAnalysis
, gsAnalysis
, gss
, gls
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