tally | R Documentation |
Tally positive and negative values from from the data.frame generated
by parseImages
by a grouping variable such as "well"
or "file"
that corresponds to a single multiplicity.
tally(df, pd = NULL, moi = NULL, by = NULL, param = "mfi")
df |
Annotated |
pd |
Optional phenotype |
moi |
Character string identifying the independent value. If |
by |
Character string identifying the grouping variable. If |
param |
Character string identifying the variable in |
The variable named positive
will be tallied for each value of
moi
(if present) represented by each level of the grouping
variable by
.
A data.frame
of tallied values for each level of the grouping
variable (typically well
or file
) with additional information
provided by the optional phenotype data. Variables generated by tally
are
expected by downstream functions. Notably, the dependent variable will
be renamed x
in the output. These variables include:
The independent variable representing the multiplicity of infection
in x
The dependent variable as the fraction of positive cells in y
The number of positive cells in pos
The number of negative in neg
Details about the grouping variable, typically well
or file
# Sample data by folder
f <- system.file("extdata", "by_folder", package = "virustiter")
pd <- read.csv(system.file("extdata", "by_folder/phenoData.csv", package = "virustiter"))
i <- getImages(f)
v <- parseImages(i)
v <- mergePdata(pd, v)
v <- score(v)
tally(v)
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