fixLinkageGroups: fixLinkageGroups - searches for discrepancies within ordered...
In oneillkza/ContiBAIT: Improves Early Build Genome Assemblies using Strand-Seq Data
Description
Usage
Arguments
Value
Description
fixLinkageGroups – searches for discrepancies within ordered contigs to highlight erroneously merged fragments.
Usage
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## S4 method for signature 'ContigOrdering,StrandStateList,LinkageGroupList'
fixLinkageGroups(contigOrdering,
orderFrame, linkageGroupList, whichLG = NULL, relatedCutOff = 0.6,
verbose = TRUE)
Arguments
contigOrdering
a data.frame of ordered contigs with linkage group names of class ContigOrdering
orderFrame
a list of StrandStateMatrix elements of class StrandStateList
linkageGroupList
List of vectors containing names of contigs belonging to each LG of type LinkageGroupList.
whichLG
vector of integers specifying the element(s) of linkageGroupList to be ordered (i.e. which specific linkage groups to try to order). Default is all LGs.
relatedCutOff
The minimal dissimilarity between adjacent contigs to subset a linkage group into multiple smaller groups. Default is 0.6
verbose
Outputs information to the terminal. Default is TRUE.
Value
a LinkageGroupList with erroneously clustered contigs seperated into their own groups
oneillkza/ContiBAIT documentation built on June 1, 2020, 5:49 a.m.
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Description Usage Arguments Value
Description
fixLinkageGroups – searches for discrepancies within ordered contigs to highlight erroneously merged fragments.
Usage
1 2 3 4 | ## S4 method for signature 'ContigOrdering,StrandStateList,LinkageGroupList'
fixLinkageGroups(contigOrdering,
orderFrame, linkageGroupList, whichLG = NULL, relatedCutOff = 0.6,
verbose = TRUE)
|
Arguments
contigOrdering |
a data.frame of ordered contigs with linkage group names of class ContigOrdering |
orderFrame |
a list of StrandStateMatrix elements of class StrandStateList |
linkageGroupList |
List of vectors containing names of contigs belonging to each LG of type LinkageGroupList. |
whichLG |
vector of integers specifying the element(s) of linkageGroupList to be ordered (i.e. which specific linkage groups to try to order). Default is all LGs. |
relatedCutOff |
The minimal dissimilarity between adjacent contigs to subset a linkage group into multiple smaller groups. Default is 0.6 |
verbose |
Outputs information to the terminal. Default is TRUE. |
Value
a LinkageGroupList with erroneously clustered contigs seperated into their own groups
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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