truePosRate: truePosRate

In OxfordCMS/OCMSutility: Utility functions for OCMS

truePosRate

Description

Calculate rate of true positives in positive control standards. Used in OCMS_zymobioimcs report.

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

Usage

truePosRate(relab, annotations, level = "species", cutoff = 0.01)

Arguments

relab	relative abundance data frame with samples in columns, features in rows
annotations	reference annotations for true positives
level	taxonomy level at which analysis is done. can be one of 'species','genus','family'. default 'species'
cutoff	threshold for read relative abundance in the sample. default is 0.01 (0.01 %)

Value

dataframe ranking features as true positive or false positive in each sample.

Examples

 # this would be better exemplified with actual std data rather than the example smaples
 data("dss_example")
data(zymobiomics)

# set count feature ids as rownames
count_df <- dss_example$merged_abundance_id %>%
  column_to_rownames('featureID')

# clean up some sample names
colnames(count_df) <- paste0('id', colnames(count_df))
tax_df <- dss_example$merged_taxonomy

# aggregate counts
agg_gen <- aggregateCount(count_df[tax_df$featureID,], tax_df, "Genus")
genus_relab <- relab(agg_gen$count_df)

true_pos_result <- truePosRate(relab=genus_relab,
                               annotations=zymobiomics$anno_ncbi_16s,
                               level='genus', cutoff=0.01)
# ->
true_pos_result <- true_pos_rate(relab=genus_relab,
                               annotations=zymobiomics$anno_ncbi_16s,
                               level='genus', cutoff=0.01)
# plot true pos rate
p <- ggplot(true_pos_result,
            aes(x=rank, y=true.pos.rate, colour=label, group=sample)) +
 geom_point() +
  theme_bw() +
  ylab("TP / (TP + FP)") +
 scale_colour_manual(values=c("grey", "purple")) +
 facet_wrap(~sample, scale="free")

p

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