tof_assess_channels: Detect low-expression (i.e. potentially failed) channels in...

In keyes-timothy/tidytof: Analyze High-dimensional Cytometry Data Using Tidy Data Principles

Detect low-expression (i.e. potentially failed) channels in high-dimensional cytometry data

Description

Detect low-expression (i.e. potentially failed) channels in high-dimensional cytometry data

Usage

tof_assess_channels(
  tof_tibble,
  channel_cols = where(tof_is_numeric),
  negative_threshold = asinh(10/5),
  negative_proportion_flag = 0.95
)

Arguments

tof_tibble	A 'tof_tbl' or 'tibble'.
channel_cols	A vector of unquoted column names representing columns that contain single-cell protein measurements. Supports tidyselect helpers. If nothing is specified, the default is to analyze all numeric columns.
negative_threshold	A scalar indicating the threshold below which a measurement should be considered negative. Defaults to the hyperbolic arcsine transformation of 10 counts.
negative_proportion_flag	A scalar between 0 and 1 indicating the proportion of cells in tof_tibble that need to be below 'negative_threshold' for a given marker in order for that marker to be flagged. Defaults to 0.95.

Value

A tibble 3 columns and a number of rows equal to the number of columns in 'tof_tibble' chosen by 'channel_cols'. The three columns are "channel", a character vector of channel names, "negative_proportion", a numeric vector with values between 0 and 1 indicating how many cells in 'tof_tibble' below 'negative_threshold' for each channel, and 'flagged_channel', a boolean vector indicating whether or not a channel has been flagged as potentially failed (TRUE means that the channel had a large number of cells below 'negative_threshold').

Examples

# simulate some data
sim_data <-
    data.frame(
        cd4 = rnorm(n = 100, mean = 5, sd = 0.5),
        cd8 = rnorm(n = 100, mean = 0, sd = 0.1),
        cd33 = rnorm(n = 100, mean = 10, sd = 0.1)
    )

tof_assess_channels(tof_tibble = sim_data)

tof_assess_channels(tof_tibble = sim_data, channel_cols = c(cd4, cd8))

tof_assess_channels(tof_tibble = sim_data, negative_threshold = 2)

keyes-timothy/tidytof documentation built on March 31, 2024, 12:01 p.m.