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Filter features in a qSIP data object

Source: R/run_feature_filter.R
run_feature_filter.Rd

Filters a feature in a feature table in a qsip_data object by presence in a minimum number of fractions and source_mat_ids.

Usage

run_feature_filter(
  qsip_data_object,
  group = NULL,
  unlabeled_source_mat_ids,
  labeled_source_mat_ids,
  min_unlabeled_sources = 2,
  min_labeled_sources = 2,
  min_unlabeled_fractions = 2,
  min_labeled_fractions = 2,
  quiet = FALSE
)

Arguments

qsip_data_object

(qsip_data) An object of qsip_data class

group

(string) An optional name to assign to this filtered group

unlabeled_source_mat_ids

(string or strings(s)) A list of the unlabeled source_mat_ids to filter on

labeled_source_mat_ids

(string or strings(s)) A list of the labeled source_mat_ids to filter on

min_unlabeled_sources

(integer, default: 2) Minimum number of unlabeled source_mat_ids a feature must be found in.

min_labeled_sources

(integer, default: 2) Minimum number of labeled source_mat_ids a feature must be found in.

min_unlabeled_fractions

(integer, default: 2) Minimum number of fractions a feature must be found in to be present in an unlabeled source_mat_id

min_labeled_fractions

(integer, default: 2) Minimum number of fractions a feature must be found in to be present in an labeled source_mat_id

quiet

(logical, default: FALSE) Suppress messages

Value

An updated qsip_data object with a filtered feature dataframe in the @filtered_feature_data slot and intermediate data in the @filter_results slot for plotting.

Details

Filtering is first done on the fractions, and then on the source_mat_ids. For example, take a feature that is found in three source_mat_ids in 3, 5 and 9 fractions. If you set min_fractions = 5 and min_sources = 3 then this feature will not survive the filtering because although it is found in three source_mat_ids, one of them is less then the minimum fraction count and would therefore be considered not found in that source_mat_id.

The feature table is filtered to retain only the feature_ids passing the filter, and to keep only the sample_ids that correspond to the given source_mat_ids. This filtered table is stored in the @filtered_feature_data slot, and the values in this table are not the raw initial values but are the relative abundances per fraction per tube. These values are originally calculated during qsip_data object creation and the values for all features are stored in the @tube_rel_abundance slot.