Function reference • bsie

All functions
`bsie`	bsie
`calc_stats_binclass()`	calc_stats_binclass returns sensitivity, specificity, positive predictive value, etc. from input true positive, true negative, false positive, false negative. from binary classification. https://en.wikipedia.org/wiki/Positive_and_negative_predictive_values#Relationship
`ciper()`	cipher Calls base::chartr to scramble input based on a set key and seed. For amino acids, single letter codes are: GPAVLIMCFYWHKRQNEDST
`collapse_df_reps()`	collapse_df_reps
`compute_breadth()`	compute_breadth
`copyTable()`	copyTable
`copyWinpath()` `copyURL()`	copyWinpath
`crossing()`	useful functions for other packages that i should remember to use more often
`deFactor()`	lapply as.character to data frame columns to convert factor to character
`foldchange()`	foldchange Calculate fold change from rpm scaled data.
`fr()`	functions for reading and writing data
`fw()`	functions for reading and writing data
`heatmapExtract()`	Input jpg heatmap, color scale, table dimensions. Output matrix of corresponding values.
`hits_score()`	hits_score
`mode_fun()`	calculate mode from numeric vector (e.g. to indicate peak of density plot) takes numeric vector, outputx x axis value of y axis peak https://stackoverflow.com/questions/13133297/calculating-peaks-in-histograms-or-density-functions ... for use in ggridges::geom_density_ridges to ignore second parameter of quantiles
`new_pro_fun()`	new_pro_fun
`pasteTable()`	pasteTable
`pasteWinpath()` `pasteURL()`	pasteWinpath gsub wrapper. By default changes \ to / from windows paths from cliboard.
`read_csv()`	functions for reading and writing data
`rml()`	rml
`rpm()`	rpm scale data frame so each column sums to 1e6 (by default)
`theme`	commonly used ggplot theme customization
`uncipher()`	uncipher Calls base::chartr to unscramble input based on a set key and seed. For amino acids, single letter codes are: GPAVLIMCFYWHKRQNEDST
`vir_evidence()`	vir_evidence Consolidate virscan hits to evidence peptides. Adapted from https://pubmed.ncbi.nlm.nih.gov/26045439/ Group hit peptides by species. Rank species by number of hits. Starting with species with most hits, for each hit peptide, remove other hit peptides with 7aa overlap from lower hit-breadth species.
`wdf()`	wdf
`zclean_longitudinal()`	zclean_longitudinal
`zscore_bins()`	zscore_bins Calculate zscores from rpm scaled data. Adapted from Michael Mina et al. 2019 DOI: 10.1126/science.aay6485

Reference

All functions