calc_group_median: Calculate medians of groups of columns

In metacoder: Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data

Calculate medians of groups of columns

Description

For a given table in a taxmap object, split columns by a grouping factor and return row medians in a table.

Usage

calc_group_median(
  obj,
  data,
  groups,
  cols = NULL,
  other_cols = FALSE,
  out_names = NULL,
  dataset = NULL
)

Arguments

obj	A taxmap object
data	The name of a table in obj$data.
groups	Group multiple columns per treatment/group. This should be a vector of group IDs (e.g. character, integer) the same length as cols that defines which samples go in which group. When used, there will be one column in the output for each unique value in groups.
cols	The columns in data to use. By default, all numeric columns are used. Takes one of the following inputs: TRUE/FALSE: All/No columns will used. Character vector: The names of columns to use Numeric vector: The indexes of columns to use Vector of TRUE/FALSE of length equal to the number of columns: Use the columns corresponding to TRUE values.
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: NULL: No columns will be added back, not even the taxon id column. TRUE/FALSE: All/None of the non-target columns will be preserved. Character vector: The names of columns to preserve Numeric vector: The indexes of columns to preserve Vector of TRUE/FALSE of length equal to the number of columns: Preserve the columns corresponding to TRUE values.
out_names	The names of count columns in the output. Must be the same length and order as cols (or unique(groups), if groups is used).
dataset	DEPRECIATED. use "data" instead.

Value

A tibble

See Also

Other calculations: calc_diff_abund_deseq2(), calc_group_mean(), 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(), zero_low_counts()

Examples

## 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 = "^(.+)__(.+)$")

# Calculate the medians for each group
calc_group_median(x, "tax_data", hmp_samples$sex)

# Use only some columns
calc_group_median(x, "tax_data", hmp_samples$sex[4:20],
                  cols = hmp_samples$sample_id[4:20])

# Including all other columns in ouput
calc_group_median(x, "tax_data", groups = hmp_samples$sex,
                  other_cols = TRUE)

# Inlcuding specific columns in output
calc_group_median(x, "tax_data", groups = hmp_samples$sex,
                  other_cols = 2)
calc_group_median(x, "tax_data", groups = hmp_samples$sex,
                  other_cols = "otu_id")

# Rename output columns
calc_group_median(x, "tax_data", groups = hmp_samples$sex,
                  out_names = c("Women", "Men"))


## End(Not run)

metacoder documentation built on April 4, 2023, 9:08 a.m.