Description Usage Arguments Value Examples
This function concatenate sequences from alignments present in the working directory based on a correspondence table and saves the output in a new directory
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df |
The user-defined correspondence table, as a data frame or equivalent. This is used only if no |
filename |
Filename of input correspondence table. Alternatively, if no filename is provided, the user can provide their own correspondence table as the |
format |
a string specifying in what formats you want the alignment |
dir |
Optional, path to the directory containing the fasta files. This argument has an effect only if fasta files names are taken from the columns of the |
plotimg |
Logical, save a graphical representation of the alignment in pdf format. Default: FALSE. |
out |
specify outputs filenames |
remove.gaps |
Logical, remove gap only columns. Useful if not using all sequences in the alignments. Default: TRUE. |
write.outputs |
Logical, save concatenated alignment, partitions position table and graphical representation. If FALSE it overrides plotimg. Default: TRUE. |
save.partitions |
Logical, save in the concatenated alignmeent directory a text file with partitions limits for the concatenated alignment. Default: TRUE. |
excel.sheet |
specify what sheet from the excel spreadsheet has to be read. Either a string (the name of a sheet), or an integer (the position of the sheet). |
The concatenated alignment (invisibly if out
is not NULL).
1 2 3 4 | dir <- system.file("extdata", package = "concatipede")
z <- concatipede(filename = paste0(dir,"/Macrobiotidae_seqnames.xlsx"), dir = dir,
write.outputs = FALSE)
z
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