Description Usage Arguments Value Author(s) References Examples
This function allows to seach for the top N differentially expressed genes or changed probes. It uses the f-values obtained using one of the following functions fcros(), fcros2(), fcrosMod(), pfco() or pfcoMod().
1 | fvalTopN(fval, topN)
|
fval |
This is a f-values vector obtained using the functions fcros(),
fcros2(), fcrosMod(), pfco() or pfcoMod(): |
topN |
The expected number of the top DE genes/probes in the dataset used. |
This function returns a data frame containing 2 components
alpha |
Two threshold values for the down- and the up-regulated allowing to have the top N DE genes |
index |
The indexes of the top N DE genes / probes |
Doulaye Dembele doulaye@igbmc.fr
Dembele D and Kastner P, Fold change rank ordering statistics:
a new method for detecting differentially expressed genes,
BMC Bioinformatics, 2014, 15:14
Dembele D and Kastner P, Comment on: Fold change rank ordering statistics: a new method for detecting differentially expressed genes, BMC Bioinformatics, 2016, 17:462
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | data(fdata);
rownames(fdata) <- fdata[,1];
cont <- c("cont01", "cont07", "cont03", "cont04", "cont08");
test <- c("test01", "test02", "test08", "test09", "test05");
log2.opt <- 0;
# perform pfco()
af <- pfco(fdata, cont, test, log2.opt);
# now select top 10 down and/or up regulated genes
top10 <- fvalTopN(af$f.value, 10);
# display thresholds
top10$alpha
# display index of top10 genes
fdata[top10$index, 1]
# display fvalue of the top10 genes
(af$f.value)[top10$index]
|
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