Description Usage Arguments Value Examples

Volcano plot for methytmle objects

1 | ```
methyvolc(x, param_bound = 2, pval_bound = 0.2)
``` |

`x` |
Object of class |

`param_bound` |
Numeric for a threshold indicating the magnitude of the size of the effect considered to be interesting. This is used to assign groupings and colors to individual CpG sites. |

`pval_bound` |
Numeric for a threshold indicating the magnitude of p-values deemed to be interesting. This is used to assign groupings and colors to individual CpG sites. |

Object of class `ggplot`

containing a volcano plot of the
estimated effect size on the x-axis and the -log10(p-value) on the y-axis.
The volcano plot is used to detect possibly false positive cases, where a
test statistic is significant due to low variance.

1 2 3 4 5 6 7 8 9 10 11 12 13 | ```
suppressMessages(library(SummarizedExperiment))
library(methyvimData)
data(grsExample)
var_int <- as.numeric(colData(grsExample)[, 1])
# TMLE procedure for the ATE parameter over M-values with Limma filtering
methyvim_out_ate <- suppressWarnings(
methyvim(
data_grs = grsExample, sites_comp = 25, var_int = var_int,
vim = "ate", type = "Mval", filter = "limma", filter_cutoff = 0.1,
parallel = FALSE, tmle_type = "glm"
)
)
methyvolc(methyvim_out_ate)
``` |

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