sumstats_orig: Computing simple summary statistics on the original data

In MultinomialMutations/MultinomialMutations: Fast multinomial regression for large cancer mutation datasets

Description

sumstats_orig computes simple summary statistics on the original data (see example) and outputs them in a pdf file for a quick check. sumstats_orig_knit_only is for a two-stage procedure where the sumstats are computed first with sumstats_orig and the pdf file is created afterwards.

Usage

sumstats_orig(inputfile, outputfile, explanatory, no_pdf_output = F)

sumstats_orig_knit_only(sumstatsfile, outputfile)

Arguments

inputfile	Character. Original data file.
outputfile	Character. Where to save the output (pdf file or Rdata file for no_pdf_output=T).
explanatory	Character vector with the names of the additional explanatory variables. See Details for the set of default variables.
no_pdf_output	Logical. Instead of the pdf output, the computed summary statistics are saved in an Rdata file.
sumstatsfile	Rdata file that contains the sumstats that were produced with the option no_pdf_output=T.

Details

R Markdown is used to create the pdf in sumstats_orig. The option no_pdf_output=T can be used to compute the summary statistics without creating the pdf. In that case, the output is saved in an Rdata file. This is useful when pandoc is not installed. Subsequently, the function sumstats_orig_knit_only can be used to knit the pdf document from the Rdata file.

The set of columns that is always assumed to be part of the data set: sample_id, from, to, count, left, right. Additional explanatory variables can vary, so they have to be set by the parameter explanatory.

Value

Nothing is returned. The output is a pdf or an Rdata file.

Author(s)

Johanna Bertl

References

Bertl, J.; Guo, Q.; Rasmussen, M. J.; Besenbacher, S; Nielsen, M. M.; Hornshøj, H.; Pedersen, J. S. & Hobolth, A. A Site Specific Model And Analysis Of The Neutral Somatic Mutation Rate In Whole-Genome Cancer Data. bioRxiv, 2017. doi: https://doi.org/10.1101/122879 http://www.biorxiv.org/content/early/2017/06/21/122879

Examples

# use system.file to find the raw dataset that was installed along with the package:
location = system.file("extdata", "set0", package = "multinomutils")

# immediately producing a pdf file
sumstats_orig(location, outputfile="~/sumstats.pdf", explanatory=c("phyloP", "replication_timing", "expression"))

# producing an Rdata file with the summary statistics ...
sumstats_orig(location, outputfile="~/sumstats.Rdata", explanatory=c("phyloP", "replication_timing", "expression"), no_pdf_output=T)
# ... and the pdf file afterwards
sumstats_orig_knit_only("~/sumstats.Rdata", outputfile="~/sumstats_knit_only.pdf")

MultinomialMutations/MultinomialMutations documentation built on May 22, 2019, 4:39 p.m.