smoother: A smoother function for coefficient values
In cshukla/oligoGames: Analyze data from massively parallel reporter assays

Description Usage Arguments Value

View source: R/DRfinder.R

This is an internal workhorse function that (optionally) smooths the coefficient values for the covariate of interest.

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smoother(y, x = NULL, weights = NULL, chr = chr,
  maxGapSmooth = maxGapSmooth, verbose = TRUE, workers = 1,
  minNum = minNum, minInSpan = minInSpan, bpSpan = bpSpan)

`x`	a vector of condition coefficients (for the covariate of interest) for each nucletide
`weights`	a numeric vector that contains the smoothing weights.
`chr`	a character vector of labels for region-level characteristics, with length equal to the number of rows in `oligo.mat` (and in the same order). This can indicate the chromosome, gene, lncRNA, etc.
`maxGapSmooth`	positive integer that indicates the maximum number of basepairs that can separate two nucleotides before they will be divided into two separate smoothing regions. Defaults to 50.
`verbose`	logical value that indicates whether addtional progress messages within each iteration should be printed to stout. Default value is FALSE.
`workers`	positive integer that represents the number of cores to use if parallelization is desired of the smoothing step.
`minNum`	positive integer that represents the minimum number of nucleotides overall in a region to be smoothed (if `smooth` is TRUE). Default value is 10
`minInSpan`	positive integer that represents the minimum number of nucleotides in a smoothing span window if `smooth` is TRUE. Default value is 10.
`bpSpan`	a positive integer that represents the length in basepairs of the smoothing span window if `smooth` is TRUE. Default value is 100

a list object of length four that contains the following objects in order: 1. fitted = a numeric matrix containing the coefficient estimates after smoothing those that satisify the smoothing conditions for each nucleotide, 2. smoothed = a logical vector that indicates whether each nucleotide was smoothed, 3. smoother = a character that represents the type of smoothing that was performed, and 4. idx a numeric vector that indicates which nucleotides are non-NULL.

cshukla/oligoGames documentation built on May 27, 2019, 8:44 a.m.