manta {manta} | R Documentation |
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.
manta(counts, samples=makeSampleDF(counts), genes=NULL, meta=NULL, meta.sum=NULL, weights=NULL, norm=TRUE, disp=TRUE, ...)
counts |
A numeric matrix containing the read counts. Rows should be named by a unique gene identifier. |
samples |
The experimental sample dataframe (nearly identical to the one in a DGEList object). |
weights |
A numberic matrix of count weights for each count. Should be the same dimentions as the count table. |
genes |
A dataframe of genes annotations that have corresponding count data. |
meta |
A taxinomic level list of gene lists of cross tabulations of taxinomic (meta) annotations for genes that have corresponding count data. |
meta.sum |
A list of aggregated counts for (one per taxinomic level). |
norm |
boolean specifiying if manta should automatically normalize using calcNormFactors(). |
disp |
boolean specifying if manta should automatically estimate the common dispersion via estimateCommonDisp(). |
... |
additional parameters passed to DGEList |
A MANTA object.
DGEList
cts.path <- system.file("extdata","PapaGO-BWA.counts-diatoms.tab", package="manta") cts <- read.delim(cts.path) samples <- makeSampleDF(cts) x <- manta(counts= cts, samples = samples)