filter_debris_cytof {Cleanet}R Documentation

Flag debris in mass cytometry data.

Description

Detect events with low distance from 0 in protein space. This function aims for high specificity, but not high sensitivity: for Cleanet's purposes, it suffices to deplete debris, even if not all of it is eliminated.

Usage

filter_debris_cytof(
  df,
  cols,
  cols_plot = c("DNA1", "CD45"),
  cofactor = 5,
  threshold = 0.3
)

Arguments

df

A data frame containing protein expression data.

cols

Columns to use in analysis. It is recommended to use the same ones in the call to cleanet.

cols_plot

Two columns that are used for visual feedback.

cofactor

Parameter for arcsinh transformation used before computing distances. 5 is a good default for mass cytometry data.

threshold

Number between 0 and 1; distances are scaled between 0 and 1 and events whose distance to the origin is smaller than the threshold are flagged.

Value

A binary array with the same length as the number of rows in df. TRUE for debris, FALSE for everything else.

Examples

path <- system.file("extdata", "df_mdipa.csv", package="Cleanet")
df_mdipa <- read.csv(path, check.names=FALSE)
cols <- c("CD45", "CD123", "CD19", "CD11c", "CD16",
          "CD56", "CD294", "CD14", "CD3", "CD20",
          "CD66b", "CD38", "HLA-DR", "CD45RA",
          "DNA1", "DNA2")
is_debris <- filter_debris_cytof(df_mdipa, cols)

[Package Cleanet version 1.0.0 Index]