pairwise.change.occupancy: find the targets whose fold changes occur consistently...

In fCI: f-divergence Cutoff Index for Differential Expression Analysis in Transcriptomics and Proteomics

Description

find the targets whose fold changes occur consistently (upregulated or downregulated) in all fCI analysis

Usage

pairwise.change.occupancy(common.ids, pairwise.index,
  pairwise.up.down, target.ratio)

Arguments

common.ids	the gene ids that are differentially expressed
pairwise.index	a list of the genes ids that differentially expressed in each of the fCI analysis
pairwise.up.down	a list of up regulatio (+1) or downregulation (-1) for each gene in fCI analysis
target.ratio	the expected fold changes

Details

TBD

Value

consistent targets	Gene (indexes) that are consistently changed in fCI pairwise analysis
direction	Gene (indexes) that are consistently upregulated (if < 0) or upregulated (if > 0)

Note

TBD

Author(s)

Shaojun Tang

References

http://software.steenlab.org/fCI/

See Also

TBD

Examples

  common.ids=6:13
  pairwise.index=list(c(4:13), c(6:15))
  pairwise.up.down=list(c(sample(c(-1,1), 10, replace=TRUE)),
                        c(sample(c(-1,1), 10, replace=TRUE)))
  target.ratio=0.5
  pairwise.change.occupancy(common.ids, pairwise.index,
    pairwise.up.down, target.ratio)

fCI documentation built on Nov. 8, 2020, 6:53 p.m.