Description Usage Arguments Value Examples

Heatmap for methytmle objects

1 |

`x` |
Object of class |

`...` |
Additional arguments passed to |

`n_sites` |
Numeric indicating the number of CpG sites to be shown in the plot. If the number of sites analyzed is greater than this cutoff, sites to be displayed are chosen by ranking sites based on their raw (marginal) p-values. |

`type` |
Whether to plot the original data (M-values or Beta-values) for the set of top CpG sites or to plot the measurements after applying a transformation into influence curve space (with respect to the target parameter of interest). The latter uses the fact that the parameters have asymptotically linear representations to obtain a rotation of the raw data into an alternative space; moreover, in this setting, the heatmap reduces to visualizing a supervised clustering procedure. |

Nothing. This function is called for its side-effect of outputting a
heatmap to the graphics device. The heatmap is constructed using the
`superheat`

package.

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"
)
)
methyheat(methyvim_out_ate, type = "raw")
``` |

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