npci.index.reconsidered {fCI} | R Documentation

## find targets that have little evidence to be differentially expressed

### Description

the function will be depreciated

### Usage

    npci.index.reconsidered(npci.data, expr.by.fold, null.data.start, diff.data.start, gene.indexes, ctr.indexes, trt.indexes, left.fold, right.fold)

### Arguments

`npci.data` | a data frame containing non-zero numeric values (the data frame must contain more than one row and one column)
`expr.by.fold` | a 1xN matrix of case-control fold changes for every gene of the total N genes
`null.data.start` | a Nx1 matrix of control-control fold changes
`diff.data.start` | a Nx1 matrix of case-control fold changes
`gene.indexes` | the genes used for differential expression analysis.
`ctr.indexes` | the control sample column indexes
`trt.indexes` | the case sample column indexes
`left.fold` | the minimum fold changes for downregulation
`right.fold` | the minimum fold changes for upregulation

### Details

TBD

### Value

`values` | genes wrongly considered as differentially expressed

### Note

TBD

### Author(s)

Shaojun Tang

### References

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

### See Also

TBD

### Examples

    data.file=data.frame(matrix(sample(3:100, 100*4, replace=TRUE), 100,4))
    wt.index=c(1,2)
    df.index=c(1,3)
    npci=new("NPCI")
    npci@wt.index=wt.index
    npci@df.index=df.index
    npci@sample.data.normalized=data.file
    npci=initialize(npci)
    npci=normalization(npci)
    npci=populate(npci)
    npci=compute(npci)
    npci=summarize(npci)

    npci.data=npci@sample.data.normalized
    null.data.start=npci@null.data.start
    diff.data.start=npci@diff.data.start
    choice=2
    rank.index.to.be.removed=npci@rank.index.to.be.removed
    expr.by.fold=npci@expr.by.fold

    ctr.indexes=1:2
    trt.indexes=3:4
    use.intersect=FALSE
    symmetric.fold=TRUE
    fold.cutoff.list=npci@fold.cutoff.list
    gene.indexes=npci@diff.gene.ids
    left.fold=2
    right.fold=2

[Package fCI version 1.20.0 Index]