cmdArgsToVariables
(Package: manta) :
Create R variables from command line parameters
Take the names of the variables specified on the R CMD BATCH call and turn them into R variables Assign the values after '=' to these variables.
● Data Source:
BioConductor
● Keywords: IO
● Alias: cmdArgsToVariables
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collapseRepliCounts
(Package: manta) :
Collapse multiple technical replicate count columns into two columns for plotting
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● Data Source:
BioConductor
● Keywords:
● Alias: collapseRepliCounts
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compbiasPlot
(Package: manta) :
plot the compositional bias for the sub-taxinomic rank
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● Data Source:
BioConductor
● Keywords:
● Alias: compbiasPlot
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compbiasTest
(Package: manta) :
compositional bias test
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● Data Source:
BioConductor
● Keywords:
● Alias: compbiasTest
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Because the manta plot uses integer count data, many of the points overlap and hide a large portion of the data. This function allows one to apply a weighting scheme to jitter points out from under each other both to show the density and expose the content of their pies (if applicable).
● Data Source:
BioConductor
● Keywords:
● Alias: generateWeights
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in2manta
(Package: manta) :
Convert a count or alignment table into a MANTA object
This function converts a table of alignment data (BLAST for example) where each record is a read and each column is some parameter of the blast(s). The function will perform a cross-tabulation of the annotated reads into count data using (at the very least) an aggregation index column and a condition column. Alternatively, the input can be pre-tabulated counts and a corresponding annotation table. The two tableMeta helper functions (called by the x2manta functions) are also documented here.
● Data Source:
BioConductor
● Keywords:
● Alias: align2manta, counts2manta, in2manta, tableMetaSums, tableMetas
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makeSampleDF
(Package: manta) :
Make a Sample Dataframe for use in Initializing a MANTA object
The sample dataframe contains a row for each sample with a factor indicating grouping and library sizes.
● Data Source:
BioConductor
● Keywords:
● Alias: makeSampleDF
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manta-class
(Package: manta) :
Microbial Assemblage Normalized Transcript Analysis - class
A simple list-based class for storing read counts from digital gene expression technologies and other important information for the analysis of (meta)transcriptomic data.
● Data Source:
BioConductor
● Keywords: classes
● Alias: manta-class
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manta
(Package: manta) :
Create a MANTA object
The MANTA object contains counts, genes, library information just like a EdgeR's DGEList. Additionally, however, it contains 'meta' annotation (typically taxinomic classifications). This function converts all of listed component elements into a MANTA object.
● Data Source:
BioConductor
● Keywords:
● Alias: manta
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meta2counts
(Package: manta) :
Convert a manta object's meta slot data into counts
This is a helper function for the mantaMethod
● Data Source:
BioConductor
● Keywords:
● Alias: meta2counts
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providing 
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