get.rscreenorm: Quantile-normalizes screen data using core sets
In rxmenezes/rscreenorm: Normalization of Multiple Genetic Screens Data

Description Usage Arguments Value See Also Examples

This is a wrapper for multiple functions, that will determine core sets and quantile-normalize scores for all replicates in a dataset.

1 2	get.rscreenorm(data_rscreen, my_gamma = NULL, var_type = c("mad", "IQR", "sd"), prop = 0.95, set_shape = c("left", "centre"), n_perc = 1000)

`data_rscreen`	an object of class 'rscreen.object', most likely corresponding to lethality scores produced by `get.leth.scores`. It is also possible to normalize re-scaled screen viability data, such as yielded by `read.screen.data`, or by `combine.screens`, although these tend to be less comparable between cell lines and replicates than the scores.
`my_gamma`	scalar or numeric vector, with value(s) between 0 and a finite number. Its default value is `NULL`. If given, it will be used to construct the core sets by using the relative distance between negative and positive controls' distributions. If a numeric vector is given, it must contain as many entries as columns in the data_only slot of data_rscreen. A value of 1 means that the core set includes all lethality scores up to the ratio between the MAD of negative controls, and the sum of the MADs of negative and positive controls, assuming the robust variability measure MAD is used.
`var_type`	string indicating the statistic used as variability measure. Possible values are 'mad' when the median absolute deviation (MAD) is used (the default), 'IQR' when the inter-quartile range is used, and "sd" when the standard deviation is used.
`prop`	scalar between 0 and 1, corresponding to the desired proportion of lethality scores to be included in the core set, per replicate. The default value is 0.95. If `my_gamma` is numeric, any value for this argument is ignored.
`set_shape`	string indicating the shape of the core set. It accepts "left" (the default), when all scores to the left of the set threshold are included, per replicate, and "centre", when scores included in the core set only exclude the largest and smallest ones, at equal frequencies.
`n_perc`	number of percentiles to be used to yield a representation of each core set. The default value is 1000, which is appropriate for pooled, whole genome screens. For small, hit-picking screens a smaller number may be more appropriate. The user may check the core set sizes to decide if in doubt. Note that the value of `n_perc` should not be larger than that of any core set.

An object of class rscreen.object, with its 'data_only' slot containing quantile-normalized lethality scores.

read.screen.data on reading screen data, combine.screens to combine data from multiple screens into a single object, get.inv.set for obtaining core sets for all replicates in the dataset and get.leth.scores to compute lethality scores.