Usage
BOGest(data, data_type, cog_file, conditional, alternative, fdr.cutoff,
gsea, gsea.fdr.alpha, DIME.K, DIME.iter, DIME.rep)
Arguments
data
This input file can be either a dataframe or a text file consisting of two
columns. The first column is the geneIDs (charaters). The second column provides numerical measures for the corresponding genes, which has
three possible options controlled by
data_type
1. data_type="data" : normalized ``differences'' of gene expressions between two comparison groups.2. data_type="raw.pval" : raw p-values for each gene if differential analysis is carried out beforehand
3. data_type="adj.pval" : multiple testing adjust
cog_file
This can either be a user specified input file (R dataframe), a raw text file, or simply the
specification of the name of one of the six built-in COGs: anthracis, brucella, coxiella, difficile, ecoli, or francisella.
conditional
For the detail, refer to description in BOG()
alternative
For the detail, refer to description in BOG()
fdr.cutoff
In statistical analysis, BOG uses local-fdr as a score for strength of evidence for differences between groups. The smaller absolute value of local fdr, the stronger is the evidence for differences in gene expression. fdr.cutoff is a threshhold used in hy
gsea
By default, gsea is set FALSE so that unless user specify it to be TRUE, BOG does not perform GSEA test.
gsea.fdr.alpha
It is the alpha used in p-value calculation in GSEA. By default, gsea.fdr.alpha=0.05
DIME.K
The number of mixture components in fitting an ensemble of mixture models. The default is 5.
DIME.iter
The number of iterations in fitting an ensemble of mixture models. The default is 50.
DIME.rep
The number of repitions in fitting an ensemble of mixture models. The default is 5.