# Selecting consensus clusters with shifting score above specified threshold

### Description

Extracts consensus clusters with shifting score and/or FDR (adjusted P-value from Kolmogorov-Smirnov test) above specified threshold. Returns their genomic coordinates, total CAGE signal and the position of dominant TSS in the two compared groups of CAGE samples, along with the value of the shifting score, P-value and FDR. Scores and P-values/FDR have to be calculated beforehand by calling `scoreShift`

function.

### Usage

1 | ```
getShiftingPromoters(object, tpmThreshold = 0, scoreThreshold = -Inf, fdrThreshold = 1)
``` |

### Arguments

`object` |
A |

`tpmThreshold` |
Consensus clusters with total CAGE signal |

`scoreThreshold` |
Consensus clusters with shifting score |

`fdrThreshold` |
Consensus clusters with adjusted P-value (FDR) from Kolmogorov-Smirnov test |

### Value

Returns a `data.frame`

of shifting promoters with genomic coordinates and positions of dominant TSS and CAGE signal in the two compared (groups of) samples, along with shifting score and adjusted P-value (FDR).

### Author(s)

Vanja Haberle

### See Also

`scoreShift`

### Examples

1 2 3 4 5 | ```
load(system.file("data", "exampleCAGEset.RData", package="CAGEr"))
shifting.promoters <- getShiftingPromoters(object = exampleCAGEset,
tpmThreshold = 100, scoreThreshold = 0.4, fdrThreshold = 0.01)
head(shifting.promoters)
``` |