bamVarName: Get library variable names from ORFik 'experiment'

In Roleren/ORFik: Open Reading Frames in Genomics

Get library variable names from ORFik experiment

Description

What will each sample be called given the columns of the experiment? A column is included if more than 1 unique element value exist in that column.

Usage

bamVarName(
  df,
  skip.replicate = length(unique(df$rep)) == 1,
  skip.condition = length(unique(df$condition)) == 1,
  skip.stage = length(unique(df$stage)) == 1,
  skip.fraction = length(unique(df$fraction)) == 1,
  skip.experiment = !df@expInVarName,
  skip.libtype = FALSE,
  fraction_prepend_f = TRUE
)

Arguments

df	an ORFik experiment
skip.replicate	a logical (FALSE), don't include replicate in variable name.
skip.condition	a logical (FALSE), don't include condition in variable name.
skip.stage	a logical (FALSE), don't include stage in variable name.
skip.fraction	a logical (FALSE), don't include fraction
skip.experiment	a logical (FALSE), don't include experiment
skip.libtype	a logical (FALSE), don't include libtype
fraction_prepend_f	a logical (TRUE), include "f" in front of fraction, useful for knowing what fraction is.

Value

variable names of libraries (character vector)

See Also

Other ORFik_experiment: ORFik.template.experiment(), ORFik.template.experiment.zf(), create.experiment(), experiment-class, filepath(), libraryTypes(), organism,experiment-method, outputLibs(), read.experiment(), save.experiment(), validateExperiments()

Examples

df <- ORFik.template.experiment()
bamVarName(df)

## without libtype
bamVarName(df, skip.libtype = TRUE)
## Without experiment name
bamVarName(df, skip.experiment = TRUE)

Roleren/ORFik documentation built on Dec. 18, 2024, 11:39 p.m.