consensusSeekeR-package
(Package: consensusSeekeR) :
consensusSeekeR: Detection of consensus peak regions inside a group of
This package compares positions and ranges data from multiple experiments to extract common consensus regions. The size of the analyzed region is adjustable as well as the number of experiments in which a peak must be detected to mark a potential region as a consensus peak region.
● Data Source:
BioConductor
● Keywords: package
● Alias: consensusSeekeR, consensusSeekeR-package
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Find regions sharing the same features for a minimum number of experiments using called peaks of signal enrichment based on pooled, normalized data (mainly coming from narrowPeak files). The peaks and narrow peaks are used to identify the consensus regions. The minimum number of experiments that must have at least on peak in a region so that it is retained as a consensus region is specified by user, as well as the size of mining regions. Only the chromosomes specified by the user are treated. The function can be parallized by specifying a number of threads superior to 1.
● Data Source:
BioConductor
● Keywords:
● Alias: findConsensusPeakRegions
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Find regions sharing the same features for a minimum number of experiments using called peaks of signal enrichment based on pooled, normalized data (mainly coming from narrowPeak files). Tje analysis is limited to one chromosome. The peaks and narrow peaks are used to identify the consensus regions. The minimum number of experiments that must have at least on peak in a region so that it is retained as a consensus region is specified by user, as well as the size of mining regions.
● Data Source:
BioConductor
● Keywords: internal
● Alias: findConsensusPeakRegionsForOneChrom
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Validation of all parameters needed by the public findConsensusPeakRegions function.
● Data Source:
BioConductor
● Keywords: internal
● Alias: findConsensusPeakRegionsValidation
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Validate if the value passed to the function is an integer or not. To be considered as an integer, the value must have a length of 1. The type of value can be a integer or numerical. However, a numerical must have the same value once casted to a integer. A vector of integers will returned FALSE.
● Data Source:
BioConductor
● Keywords: internal
● Alias: isInteger
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readNarrowPeakFile
(Package: consensusSeekeR) :
Extract narrow regions and peaks from a narrrowPeak file
Read a narrowPeak file and extract the narrow regions and/or the peaks, as specified by used. The narrowPeak file must fit the UCSC specifications. See https://genome.ucsc.edu/FAQ/FAQformat.html#format12 for more details. The file can have one or many header lines. However, the total number of header lines must be inferior to 250 lines.
● Data Source:
BioConductor
● Keywords:
● Alias: readNarrowPeakFile
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refineRegion
(Package: consensusSeekeR) :
Refine the selected region by using an iterative process.
Find regions sharing the same features for a minimum number of experiments using called peaks of signal enrichment based on pooled, normalized data (mainly coming from narrowPeak files). Tje analysis is limited to one chromosome. The peaks and narrow peaks are used to identify the consensus regions. The minimum number of experiments that must have at least on peak in a region so that it is retained as a consensus region is specified by user, as well as the size of mining regions.
● Data Source:
BioConductor
● Keywords: internal
● Alias: refineRegion
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providing 
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