Function reference • AbNames

All functions

addID(): add ID column

dashNotDot(): Convert dashes (-) to dots(.)

defaultQuery(): Default list of functions for making an antibody query table

.checkSubunitMatches(): Check if all subunits of a multi-subunit protein are matched Internal AbNames function for removing spurious matches caused by guessing subunit names. Column names are hard-coded and expected to match the default pipeline. Returns a table containing gene name matches with spurious matches removed.

.freducePartial(): Create a list of partial functions and apply in sequence

.getGroups(): Return the first n groups of a grouped data.frame

.printGroupMatch(): Select a group from a data.frame, format into a printable string

.printf(): Wrapper for sprintf, doesn't convert NA to character

.separateSubunits(): Separate multi-subunit protein names into one name per row

.sharedSubstr(): Group based on shared substrings

.stopIfColExists(): Warn if a column already exists in a data.frame

.tempColName(): Create a name for a temporary column in a data.frame

.toString(): Wrapper for toString, doesn't convert NA to character and only concatenates unique values

fillByGroup(): Fill NAs in data.frame by grouping

filter_by_union(): Select rows matching any column present in another data.frame

formatIg(): Format immunoglobin antibody names

formatTCR(): Convert T-cell receptor antigen names

formatTCRv(): Format TCR (vector)

gene_aliases: Gene names, symbols and IDs from HGNC, Entrez and Ensembl

groupMode(): Find the most common value per group

gsubAb(): Convenience function to remove a pattern from a column in a data.frame

hgnc: Gene names, symbols and IDs from HGNC, in long format

lowerNoDash(): Convert values to lowercase and replace - with space

makeQueryTable(): Separate Antibody/Antigen names into component parts

matchToCiteseq(): Standardise names using the citeseq data set

nPerGroup(): Group a data.frame and count unique values

replaceGreekSyms(): Replace Greek symbols or symbol names

searchAliases(): Search for matches to antibody names in gene aliases data set

searchTotalseq(): Annotate gene IDs using totalseq data set

separateSubunits(): Separate multi-subunit protein names

sharedSubstr(): Group based on shared substrings

showGroups(): Interactively print individual groups of a grouped data.frame

splitMerge(): Apply a function to a subset of a data.frame

splitUnnest(): Split a column and create one row per entry

totalseq: Antibody and gene information for TotalSeq antibodies from BioLegend

upperSquish(): Convert values to uppercase and remove punctuation