Description Usage Arguments Details Value Examples
This function will plot the first few mafs in the dataset overlaid with a smooth version of the same maf and, if desired, confidence intervals. Additionally, an estimate of the number of mafs will be printed.
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cexVal |
The size of the labels in the plot |
B |
Number of replications in the confidence interval calculations |
alpha |
The significance level |
block.size |
The block size of the resampled residuals, i.e. the number of contiguous time steps to sample at the time from the set of residuals. |
maf.object |
The output of the |
smoothSpan |
Fraction between 0-1 that specifies the proportion of timesteps to include in the smoothing window, which is weighted by a tricubic. See ?loess for details. Alternatively, one can specify an integer greater than 1 which refers to the number of time points to include in the tricubic filter. |
nmaf |
The number of MAFs to plot |
with.wncertainty |
A logical specifying whether to plot the confidence interval around each maf. |
The confidence intervals are obtained using a resampling scheme which extracts the residuals of the original
time series after smoothing
with the same filter as the one parametrized by smoothSpan
. The residuals are
bootstrapped or block bootstrapped (if there is temporal structure in the residuals)
and added back to the smooth, creating a new data set. From the new data set a new set of
MAFs are calculated.
The smoothing parameter smooth.span
is also used when calculating the empirical
Signal-to-Noise ratio. Where we subtract the smooth from the time series and calculate
the variance of the smooth estimate over the residual variance. This gives an empirical
signal-to-noise estimate.
A plot of the MAFs and a list containing
statStar
Empirical SNR for each resampled MAF time series, i.e. a p x B matrix where p is the total number of predictors and B is the number of bootstraps/replications
statObs
The empirical SNR of the original MAF time series.
pval
The p-values of each MAF, where the p-value refers to the number of resampled MAFs that have a higher empirical SNR than the original MAFs. If there are less than α, e.g. 0.05, resampled MAFs that have a higher empirical SNR than the original MAF, the MAF in question is not significant.
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