Description Usage Arguments Value Author(s) See Also Examples
Filters the columns of the input data, i.e., positions of input sequences,
by a filter function that, given a DLData object, returns a list containing
i) as element $selected
a vector with entries TRUE
for every column
that should be retained in the filtered data and ii) as element $range
the
range of values obtained for the filtering criterion.
1 | filterColumns(data, filter.fun)
|
data |
the data as DLData object |
filter.fun |
the filter function |
a DLData object containing the filtered columns and the indexes of the remaining in its axis.labels
field
Jan Grau <grau@informatik.uni-halle.de>
filter.by.gaps
filter.by.dependencies
filter.by.conservation
1 2 3 4 5 6 7 8 | # read data and create DLData object
seqs <- read.table(system.file("extdata", "cjun.txt", package = "DepLogo"),
stringsAsFactors = FALSE)
data <- DLData(sequences = seqs[, 1], weights = log1p(seqs[, 2]) )
# create a filter function based on the percentage of gap symbols (at most 10%)
fun <- filter.by.gaps(percent.gap = 0.1)
data2 <- filterColumns(data, fun)
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