Batch and confounding diagnostics — batch

Checks whether the study design, the quality-control metrics and the main axes of variation follow technical batches such as cartridges and run dates.

Usage

batch_diagnostics(x, group = NULL, batch = c("CartridgeID", "Date"))

Arguments

x: A nacho object from load_rcc() or normalise().
group: A column of nacho_samples(x) with the biological groups, or NULL to skip the design check.
batch: Columns of nacho_samples(x) that describe technical batches.

Value

A list:

design: NULL without group; otherwise, for each batch variable, its number of levels, Cramér's V with group, the number of levels that hold a single group, and confounded, TRUE when at least one does. A level counts as holding a single group only when it has two or more samples with a group, so a cartridge with one sample never makes the design confounded. Cramér's V uses only the samples that have both a group and a batch, and is NA when the batch or group has fewer than two levels among them.
crosstabs: NULL without group; otherwise the table of group against each batch variable.
metrics: Kruskal-Wallis tests of each quality-control metric against each batch variable.
pc_batch: the share of each principal component's variance explained by each batch variable.

metrics and pc_batch are data frames with these columns, and have no rows when there is nothing to report. A batch variable with one level gives NA in statistic, p_value and r_squared, and a constant metric gives NA in statistic and p_value. A batch variable whose levels each hold one sample with a value also gives NA in r_squared. For PlexSet data, BD and FoV are tested once per lane.

Details

Start with design: when a batch level holds a single group, batch and biology cannot be told apart, and no normalisation can fix it.

Examples

data(GSE74821)
batch_diagnostics(GSE74821)$pc_batch
#>      PC       batch    r_squared
#> 1  PC01 CartridgeID 8.669160e-03
#> 2  PC02 CartridgeID 1.812515e-01
#> 3  PC03 CartridgeID 1.482027e-02
#> 4  PC04 CartridgeID 1.697497e-01
#> 5  PC05 CartridgeID 6.387001e-02
#> 6  PC06 CartridgeID 4.405153e-02
#> 7  PC07 CartridgeID 5.334040e-02
#> 8  PC08 CartridgeID 3.552575e-02
#> 9  PC09 CartridgeID 1.007797e-01
#> 10 PC10 CartridgeID 1.599434e-01
#> 11 PC01        Date 4.242826e-03
#> 12 PC02        Date 4.119176e-02
#> 13 PC03        Date 1.343894e-03
#> 14 PC04        Date 7.225959e-02
#> 15 PC05        Date 1.169531e-02
#> 16 PC06        Date 2.831487e-02
#> 17 PC07        Date 5.279313e-02
#> 18 PC08        Date 6.286744e-05
#> 19 PC09        Date 2.957369e-02
#> 20 PC10        Date 1.090615e-02