select_rows: Flexibly select rows of a data frame.
In PerkinElmer/phenoptr: inForm Helper Functions

Description Usage Arguments Details Value See Also Examples

Select rows of a data frame based on phenotypes or other expressions.

1	select_rows(csd, sel)

`csd`	A data frame
`sel`	May be a character vector, a one-sided formula, a list containing such or `NA`. A character vector is interpreted as the name(s) of one or more phenotypes and selects any matching phenotype. A formula is interpreted as an expression on the columns of `csd`. Multiple list items are joined with AND. `NA` is interpreted as "select all". It is convienent for lists of selection criteria.

select_rows implements a flexible mechanism for selecting cells (rows) from a cell segmentation table. Cells may be selected by single or multiple phenotype, by expression level, or combinations of both.

See the tutorial Selecting cells within a cell segmentation table for extensive documentation and examples.

A logical vector of length nrow(csd) which selects rows according to sel.

parse_phenotypes for a convenient way to create selectors for most common phenotypes.

csd <- sample_cell_seg_data

# Select tumor cells with PDL1 expression > 3
selector <- list('CK+', ~`Entire Cell PDL1 (Opal 520) Mean`>3)
pdl1_pos_tumor <- csd[select_rows(csd, selector),]
range(pdl1_pos_tumor$`Entire Cell PDL1 (Opal 520) Mean`)

# Select all T-cells. Note: Use c() to combine phenotypes, not list()
selector <- c('CD8+', 'FoxP3+')
tcells <- csd[select_rows(csd, selector),]
table(tcells$Phenotype)