calculatePosteriorAvg: Calculate the posterior average for indicators of concordant...

Description Usage Arguments Details Value Author(s) See Also

View source: R/functions.R


This function calculates the posterior average for indicators of concordant and discordant differential expression from the saved log files. See details.


calculatePosteriorAvg(object, NCONC=2, NDIFF=1, burnin=0)



Object of class XdeMcmc


Integer: number of studies for which the gene must be differentially expressed (in the same direction) to be classified as concordant differential expression


Integer: number of studies for which a gene must be up- or down-regulated to be classified as differentially expressed. It is the union of concordant and discordant differential expression.


Integer: number of MCMC iterations for the burnin. Posterior means are computed from the MCMC samples following burnin.


For each iteration,

1. calculate the sign of delta * Delta

2. For each gene, compute the number of positive signs (P) and the number of negative signs (N) (a G x 2 matrix, where G is the number of genes in common across all studies). P + N is <= S, where S is the number of studies.

3. for a given gene, the discordant indicator is simply when P * N is nonzero.

4. The concordant indicator requires P * N = 0 AND P + N >= NCONC, where NCONC is specified by the user.

5. differential expression is simply | P | + | N | >= NDIFF. By default, NDIFF is 1 but can be user-specified.

The posterior average is then computed from the mean over all MCMC iterations.


A G x 3 matrix.



See Also


XDE documentation built on Nov. 8, 2020, 5:02 p.m.