filter_by_data(exp, predicate[, axis, …]) |
Filter samples or features by the data matrix. |
filter_by_metadata(exp, field, select[, …]) |
Filter samples or features by metadata. |
filter_samples(exp, field, values[, negate, …]) |
Shortcut for filtering samples. |
filter_ids(exp, ids[, axis, negate, inplace]) |
Filter samples or features based on a list IDs. |
filter_prevalence(exp, fraction[, cutoff, field]) |
Filter features keeping only ones present in more than certain fraction of all samples. |
filter_abundance(exp[, cutoff]) |
Filter features with sum abundance across all samples less than the cutoff. |
filter_mean_abundance(exp[, cutoff, field]) |
Filter features with a mean at least cutoff of the mean total abundance/sample |
filter_sample_categories(exp, field[, …]) |
Filter sample categories that have too few samples. |
downsample(exp, field[, axis, num_keep, …]) |
Downsample the data set. |
is_abundant(data, axis[, cutoff, strict, …]) |
Check if the mean or sum abundance larger than cutoff. |
is_prevalent(data, axis[, cutoff, fraction]) |
Check the prevalent of values above the cutoff. |
freq_ratio(x[, ratio]) |
the ratio of the counts of the most common value to the second most common value |
unique_cut(x[, unique]) |
the percentage of distinct values out of the length of x. |
