filterFeature: filterFeature.R

In OxfordCMS/OCMSutility: Utility functions for OCMS

filterFeature.R

Description

filter out reads based on cutoff threshold and asv prevalence across samples

filterFeature was renamed to filter_feature for more consistent function naming nomenclature in OCMSutility. Usage is still exactly the same

Usage

filterFeature(
  count_df,
  tax_df,
  filter_method = "abs_count",
  asv_cutoff = 1,
  prev_cutoff = 2
)

Examples

data(dss_example)

# put featureID as rownames
tax_df <- dss_example$merged_taxonomy
count_df <- dss_example$merged_abundance_id %>%
  column_to_rownames('featureID')
# set features in count tax to be in same order
count_df <- count_df[tax_df$featureID,]

filtered_ls <- filterFeature(count_df, tax_df, 'percent_sample', 0.001, 2)
# ->
filtered_ls <- filter_eature(count_df, tax_df, 'percent_sample', 0.001, 2)
summary(filtered_ls)
filtered_count <- filtered_ls$filtered
dim(filtered_count)
head(filtered_count)

OxfordCMS/OCMSutility documentation built on Feb. 27, 2025, 8:19 p.m.