Description Usage Arguments Value Examples

View source: R/replicate_correlation.R

'replicate_correlation' measures replicate correlation of variables.

1 2 | ```
replicate_correlation(sample, variables, strata, replicates,
replicate_by = NULL, split_by = NULL, cores = NULL)
``` |

`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 |

data frame of variable quality measurements

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 | ```
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::data_frame(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)
``` |

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