replicate_correlation: Measure replicate correlation of variables.

In cytominer: Methods for Image-Based Cell Profiling

Description

'replicate_correlation' measures replicate correlation of variables.

Usage

replicate_correlation(
  sample,
  variables,
  strata,
  replicates,
  replicate_by = NULL,
  split_by = NULL,
  cores = NULL
)

Arguments

sample	tbl containing sample used to estimate parameters.
variables	character vector specifying observation variables.
strata	character vector specifying grouping variables for grouping prior to normalization.
replicates	number of replicates.
replicate_by	optional character string specifying column containing the replicate id.
split_by	optional character string specifying column by which to split the sample into batches; replicate correlations will be calculate per batch.
cores	optional integer specifying number of CPU cores used for parallel computing using doParallel.

Value

data frame of variable quality measurements

Examples

set.seed(123)
x1 <- rnorm(10)
x2 <- x1 + rnorm(10) / 100
y1 <- rnorm(10)
y2 <- y1 + rnorm(10) / 10
z1 <- rnorm(10)
z2 <- z1 + rnorm(10) / 1

batch <- rep(rep(1:2, each = 5), 2)

treatment <- rep(1:10, 2)

replicate_id <- rep(1:2, each = 10)

sample <-
  tibble::tibble(
    x = c(x1, x2), y = c(y1, y2), z = c(z1, z2),
    Metadata_treatment = treatment,
    Metadata_replicate_id = replicate_id,
    Metadata_batch = batch
  )

head(sample)

# `replicate_correlation`` returns the median, min, and max
# replicate correlation (across batches) per variable
replicate_correlation(
  sample = sample,
  variables = c("x", "y", "z"),
  strata = c("Metadata_treatment"),
  replicates = 2,
  split_by = "Metadata_batch",
  replicate_by = "Metadata_replicate_id",
  cores = 1
)

Example output

Attaching package: ‘cytominer’

The following object is masked from ‘package:stats’:

    aggregate

The following object is masked from ‘package:base’:

    transform

# A tibble: 6 x 6
        x      y      z Metadata_treatment Metadata_replicate_id Metadata_batch
    <dbl>  <dbl>  <dbl>              <int>                 <int>          <int>
1 -0.560  -1.07  -0.695                  1                     1              1
2 -0.230  -0.218 -0.208                  2                     1              1
3  1.56   -1.03  -1.27                   3                     1              1
4  0.0705 -0.729  2.17                   4                     1              1
5  0.129  -0.625  1.21                   5                     1              1
6  1.72   -1.69  -1.12                   6                     1              2
# A tibble: 3 x 4
  variable median   min   max
  <chr>     <dbl> <dbl> <dbl>
1 x         1.00  1.00  1.00 
2 y         0.996 0.993 0.999
3 z         0.627 0.290 0.964

cytominer documentation built on July 8, 2020, 5:08 p.m.