zero_low_counts | R Documentation |
For a given table in a taxmap
object, convert all counts
below a minimum number to zero. This is useful for effectively removing
"singletons", "doubletons", or other low abundance counts.
zero_low_counts(
obj,
data,
min_count = 2,
use_total = FALSE,
cols = NULL,
other_cols = FALSE,
out_names = NULL,
dataset = NULL
)
obj |
A |
data |
The name of a table in |
min_count |
The minimum number of counts needed for a count to remain
unchanged. Any could less than this will be converted to a zero. For
example, |
use_total |
If |
cols |
The columns in
|
other_cols |
Preserve in the output non-target columns present in the input data. New columns will always be on the end. The "taxon_id" column will be preserved in the front. Takes one of the following inputs:
|
out_names |
The names of count columns in the output. Must be the same
length and order as |
dataset |
DEPRECIATED. use "data" instead. |
A tibble
Other calculations:
calc_diff_abund_deseq2()
,
calc_group_mean()
,
calc_group_median()
,
calc_group_rsd()
,
calc_group_stat()
,
calc_n_samples()
,
calc_obs_props()
,
calc_prop_samples()
,
calc_taxon_abund()
,
compare_groups()
,
counts_to_presence()
,
rarefy_obs()
## Not run:
# Parse data for examples
x = parse_tax_data(hmp_otus, class_cols = "lineage", class_sep = ";",
class_key = c(tax_rank = "taxon_rank", tax_name = "taxon_name"),
class_regex = "^(.+)__(.+)$")
# Default use
zero_low_counts(x, "tax_data")
# Use only a subset of columns
zero_low_counts(x, "tax_data", cols = c("700035949", "700097855", "700100489"))
zero_low_counts(x, "tax_data", cols = 4:6)
zero_low_counts(x, "tax_data", cols = startsWith(colnames(x$data$tax_data), "70001"))
# Including all other columns in ouput
zero_low_counts(x, "tax_data", other_cols = TRUE)
# Inlcuding specific columns in output
zero_low_counts(x, "tax_data", cols = c("700035949", "700097855", "700100489"),
other_cols = 2:3)
# Rename output columns
zero_low_counts(x, "tax_data", cols = c("700035949", "700097855", "700100489"),
out_names = c("a", "b", "c"))
## End(Not run)
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