get.pvals.DF: Permutation-based significance tests for differentially...

In leekgroup/derfinder: Differential expression analysis of RNA-seq data at base-pair resolution

Description

Creates simulated null distribution of average t statistics for regions classified as over- or underexpressed, and obtains p-values for observed over- and underexpressed regions based on this simulated null.

Usage

get.pvals.DF(regions, num.perms = 1, est.params, chromosome,
  verbose = FALSE, DF, comparison = c("twogroup", "multigroup",
  "expression"), group, chunksize = 1e+05, adjustvars = NULL,
  colsubset = NULL, scalefac = 32, nonzero = FALSE)

Arguments

regions	data frame of regions to obtain p-values for: specifically the $states element of the return of getRegions. Must have mean.t and state columns.
num.perms	Number of permutations to use to create the null distribution.
est.params	return from getParams - HMM parameters used when creating regions
chromosome	Chromosome you are analyzing. Currently only runs one chromosome at a time.
verbose	If TRUE statements with status updates are printed at each permutation.
DF	A list containing a DF DataFrame with the coverage data and a logical Rle with the positions that passed the cutoff. This object is generated using makeDF.
comparison	Either twogroup, multigroup or expression. multigroup will use the F-statistic and expression tests the intercept-only model.
group	0/1 vector denoting group labels for the samples used in analysis. Should have the same length as colsubset if colsubset is specified.
chunksize	How many rows of the merged table should be processed at a time?
adjustvars	Optional matrix of adjustment variables (e.g. measured confounders, output from SVA, etc.) to use in fitting linear models to each nucleotide.
colsubset	Optional vector of column indices of the input file that denote samples you wish to include in analysis.
scalefac	A log transformation is used on the count tables, so zero counts present a problem. What number should we add to the entire matrix before running the models? Defaults to 32.
nonzero	If TRUE, use the median of only the nonzero counts as the library size adjustment.

Value

A vector having length equal to the number of rows in regions, giving a p-value for each region of state 3 or 4 in regions.

Author(s)

Alyssa Frazee, Leonardo Collado-Torres

See Also

getLimmaInput.DF,getTstats,getRegions

leekgroup/derfinder documentation built on May 20, 2019, 11:30 p.m.