isSignificant {qsea} | R Documentation |
This function looks for regions, where the test statistic is below the defined thresholds
isSignificant(glm, contrast = NULL, fdr_th = NULL, pval_th = NULL, absLogFC_th = NULL, direction = "both")
glm |
A qseaGLM object (mandatory) |
contrast |
name of contrast to be used |
fdr_th |
a threshold for the false discovery rate |
pval_th |
a p value threshold |
absLogFC_th |
the threshold for the absolute value of logFC |
direction |
direction of change: either "both", "loss", or "gain" |
If a threshold is NULL, it is ignored.
For the direction parameter, the following synonyms are valid:
"loss" == "less" == "hypo"
"gain" == "more" == "hyper"
A vector with indices of significant windows, which can be passed to keep parameter of makeTable() function
Mathias Lienhard
makeTable
qs=getExampleQseaSet() design=model.matrix(~group, getSampleTable(qs)) TvN_glm=fitNBglm(qs, design, norm_method="beta") TvN_glm=addContrast(qs,TvN_glm, coef=2, name="TvN") sig=isSignificant(TvN_glm, fdr_th=0.01)