getColmeds: Calculate the medians of the database.

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

Description

getColmeds calculates the median of the samples of interest from the database table. It is used in getLimmaInput and it's output can be saved to avoid calculating it multiple times when running get.pvals.

Usage

getColmeds(dbfile, tablename, colsubset = c(-1), nonzero = FALSE)

Arguments

dbfile	Name/location (as character string) of database (usually ".db") file containing nucleotide by sample coverage.
tablename	Name of the table the database contains
colsubset	Optional vector of column indices of the input file that denote samples you wish to include in analysis. Should NEVER include 1 (genomic position).
nonzero	If TRUE, use the median of only the nonzero counts as the library size adjustment.

Details

It is assumed that the first column in the database is called pos and contains genomic position. Note that "group" must have the one fewer entries than the database denoted by dbfile has columns (or, if colsubset is used, one fewer entries than the length of colsubset).

Value

A vector with the column medians.

Author(s)

Alyssa Frazee. Code split from getLimmaInput by Leonardo Collado-Torres.

See Also

getLimmaInput

Examples

## add example here when we have a vignette

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