above_threshold: Calculate number of observations above a certain threshold
In tkostas/komics: Tools to analyze omics data

Description Usage Arguments Value Examples

Reads a data frame and calculates the number of observations that are above a certain threshold value. Frequency is calculated for columns or rows. Groups can be assigned in the group_ids argument, by passing a list with the corresponding info (see arguments).

1	above_threshold(x, apply_to = "columns", group_ids = NULL, threshold = 0)

`x`	A dataframe. You can select which columns to be used using the group_ids argument.
`apply_to`	Character vector. Calculate frequency for "columns", or "rows". Default value is "columns".
`group_ids`	List of group names and group identifiers (see example). If all the columns are used as one group, skip this argument. To specific columns for one or more groups define a list in which the name of each list element will be the group name and every element will contain a character vector that matches with the column names of the specific group. Matching of the columns can be partial (e.g. ctrl_ to select multiple columns containing the "ctrl_" character string)
`threshold`	The minimum value to calculate frequency. Default is 0.

Output is a list and each element is a vector containing the sum of observations that are above the threshold. Each element has the same name as it was defined in the group_ids list, and omitting naming the elements of the list will return an error. This way you can calculate frequencies for different groups in parallel.

treatment_group <- c("Tretment", "treated")
control_group <- c("ctrl", "control")
group_ids <- list(treatment = treatement_group,
                  control = control_group)

above_threshold(data, group_ids = group_ids, threshold = 0)