View source: R/shuffleMutations.R
A function to check if the parameters are correct of the
shuffleMutations
function
1 2 3 4 5 6 | checkParametersShuffleMutations(dataTable, chromHeader, positionHeader,
refHeader, altHeader, contextHeader, sampleIdHeader, nBootstrap,
maxDistance, reverseComplement, searchPatterns, searchRefHeader,
searchAltHeader, searchContextHeader, searchIdHeader,
searchDistanceHeader, searchReverseComplement, asTibble,
returnEachBootstrap, searchClusterPatterns, no.cores, linkPatterns)
|
dataTable |
A table with the reference, alternative and surrounding
nucleotides. The best data to use is the output of the
|
chromHeader |
A string with the name of the column with the chromosome name. (So the data in the column needs to be notated as e.g. "chr2") |
positionHeader |
A string with the name of the column with the position of the mutation. (The data in the column needs to be nummeric.) |
refHeader |
A string with the column header of the reference nucleotide. |
altHeader |
A string with the column header of the alternative nucleotide. |
contextHeader |
A string with the column header of the context nucleotides. |
sampleIdHeader |
A string with the name of the column with the sample ID. |
nBootstrap |
A number with the amount of bootstraps there need to be executed. |
maxDistance |
A number with the maximum distance between DNA mutations that are defined as being in a cluster. |
reverseComplement |
A Boolean to tell if the |
searchPatterns |
A tibble with the known mutation patterns. The
|
searchRefHeader |
A string with the column name of the one with the reference nucleotide in the searchPatterns table. |
searchAltHeader |
A string with the column name of the one with the alternative nucleotide in the searchPatterns table. |
searchContextHeader |
A string with the column name of the one with the context nucleotide in the searchPatterns table. |
searchIdHeader |
A string with the column name of the one with the pattern IDs. |
searchDistanceHeader |
A string with the column name of the one with the maximum distance between clustered mutations. Not needed if the distance parameter is NULL. NA's within this column are allowed. |
searchReverseComplement |
A boolean to also search the patterns in the reverse complement of the searchPatterns tibble. |
asTibble |
A Boolean if the returned results needs to be a tibble. It
will return a data.frame otherwise. Irrelevant if |
returnEachBootstrap |
A Boolean if the summaries per bootstrap are needed to be returned. If TRUE then the return value will be a list with a summary of each bootstrap. |
searchClusterPatterns |
A Boolean if it's needed to search to cluster patterns (e.g. GA > TT). |
no.cores |
A number with the amount of clusters that is allowed to use during shuffle. Default is maximum amount of cores present on the system. |
linkPatterns |
A Boolean to tell if it's necessary to try and link the
mutations to patterns. If FALSE then the |
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