significance_subset function

Extract a subset population

Subsets data according to the significance groups.

significance_subset(polar, significance = NULL, output = "pvals")

Arguments

• polar: A polar object including expression data from groups of interest. Created by polar_coords.

• significance: Which significance factors to subset to. If NULL

  all levels except 'ns' (non-significant) are selected.

• output: What object to return. Options are "pvals", "padj", "data", "df" for subset dataframes, or "polar" to subset the entire 'volc3d' class object.

Returns

Returns an object (type defined by output) with rows susbet to those which satisfy the significance condition.

Examples

data(example_data)
syn_polar <- polar_coords(outcome = syn_example_meta$Pathotype,
                          data = t(syn_example_rld))

subset <- significance_subset(syn_polar, "L+", "df")

References

Lewis, Myles J., et al. (2019). c("\n", "Molecular portraits of early rheumatoid arthritis identify clinical and\n", "treatment response phenotypes.")

Cell reports, 28 :9