selectLoci


    The <code><a rd-options="" href="/link/lociData?package=segmentSeq&version=2.6.0" data-mini-rdoc="segmentSeq::lociData">lociData</a></code> object to be filtered.
  


  If provided, all loci with a likelihood greater than this criterion
  will be selected.


likelihood


  If provided (and likelihood is not provided), the maximal set of
  loci which controls the FDR at this level is selected.



  If provided (and likelihood and FDR are not provided), the maximal set of
  loci which controls the FWER at this level is selected.


FWER


  If TRUE, selection of loci is done on a replicate by replicate
  basis. If FALSE, selection will be done on the likelihood that the
  locus represents a true locus in at least one replicate group.


perReplicate


  Selects loci from a `lociData' object based on likelihood, false
  discovery rate or familywise error rate for downstream processing.


manip

High-throughput sequencing technologies allow the production of large volumes of short sequences, which can be aligned to the genome to create a set of matches to the genome. By looking for regions of the genome which to which there are high densities of matches, we can infer a segmentation of the genome into regions of biological significance. The methods in this package allow the simultaneous segmentation of data from multiple samples, taking into account replicate data, in order to create a consensus segmentation. This has obvious applications in a number of classes of sequencing experiments, particularly in the discovery of small RNA loci and novel mRNA transcriptome discovery.

Thomas J Hardcastle

segmentSeq

Methods for identifying small RNA loci from high-throughput
sequencing data

selectLoci function

The <code><a href="lociData" rd-options="">lociData</a></code> object to be filtered.

If provided, all loci with a likelihood greater than this criterion
  will be selected.

If provided (and likelihood is not provided), the maximal set of
  loci which controls the FDR at this level is selected.

If provided (and likelihood and FDR are not provided), the maximal set of
  loci which controls the FWER at this level is selected.

If TRUE, selection of loci is done on a replicate by replicate
  basis. If FALSE, selection will be done on the likelihood that the
  locus represents a true locus in at least one replicate group.

Selects loci from a `lociData' object based on likelihood, false
  discovery rate or familywise error rate for downstream processing.

selectLoci: Filters a `lociData' object based on given selection criteria.

Description

Usage

Arguments

Value

See Also