Description Usage Arguments Value Author(s) Examples

The function finds the highest smoothed score cutoff for a pre-specified FDR. Smoothing is performed over a specified number of basepairs, and regions must have a minimum number of qualifying probes to be considered significant. The FDR is calculated as the ratio of the number of significant regions found in a permutation-based test, to the number found in the actual experimental microarray data.

1 2 3 4 | ```
## S4 method for signature 'matrix'
regionStats(x, design = NULL, maxFDR=0.05, n.perm=5, window=600, mean.trim=.1, min.probes=10, max.gap=500, two.sides=TRUE, ndf, return.tm = FALSE, verbose=TRUE)
## S4 method for signature 'AffymetrixCelSet'
regionStats(x, design = NULL, maxFDR=0.05, n.perm=5, window=600, mean.trim=.1, min.probes=10, max.gap=500, two.sides=TRUE, ind=NULL, return.tm = FALSE, verbose=TRUE)
``` |

`x` |
An |

`design` |
A design matrix of how to manipulate |

`maxFDR` |
Cutoff of the maximum acceptable FDR |

`n.perm` |
Number of permutations to use |

`window` |
Size of window, in base pairs, to check for |

`mean.trim` |
A number representing the top and bottom fraction of ordered values in a window to be removed, before the window mean is calculated. |

`min.probes` |
Minimum number of probes in a window, for the region to qualify as a region of significance. |

`max.gap` |
Maximum gap between significant probes allowable. |

`two.sides` |
Look for both significant positive and negative regions. |

`ind` |
A vector of the positions of the probes on the array |

`ndf` |
The Nimblegen Definition File for Nimblegen array data. |

`return.tm` |
If TRUE, the values of the trimmed means of the intensities and permuted intensities are also retuned from the function. |

`verbose` |
Whether to print the progress of processing. |

A `RegionStats`

object (list) with elements

`regions` |
A list of |

`tMeanReal` |
Matrix of smoothed scores of intensity data. Each column is an experimental design. |

`tMeanPerms` |
Matrix of smoothed scores of permuted intensity data. Each column is an experimental design. |

`fdrTables` |
List of table of FDR at different score cutoffs. Each list element is for a different experimental design. |

Mark Robinson

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 | ```
## Not run:
library(Repitools)
library(aroma.affymetrix)
# assumes appropriate files are at annotationData/chipTypes/Hs_PromPR_v02/
cdf <- AffymetrixCdfFile$byChipType("Hs_PromPR_v02",verbose=-20)
cdfU <- getUniqueCdf(cdf,verbose=-20)
# assumes appropriate files are at rawData/experiment/Hs_PromPR_v02/
cs <- AffymetrixCelSet$byName("experiment",cdf=cdf,verbose=-20)
mn <- MatNormalization(cs)
csMN <- process(mn,verbose=-50)
csMNU <- convertToUnique(csMN,verbose=-20)
#> getNames(cs)
# [1] "samp1" "samp2" "samp3" "samp4"
design <- matrix( c(1,-1,rep(0,length(cs)-2)), ncol=1, dimnames=list(getNames(cs),"elut5_L-P") )
# just get indices of chr7 here
ind <- getCellIndices(cdfU, unit = indexOf(cdfU, "chr7F"), unlist = TRUE, useNames = FALSE)
regs <- regionStats(csMNU, design, ind = ind, window = 500, verbose = TRUE)
## End(Not run)
``` |

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