pairwise.change.occupancy {fCI} | R Documentation

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

### 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)

[Package fCI version 1.20.0 Index]