create_matrices: Given a samples sheet with some metadata, create a big pile...

In abelew/Rerrrt: Examine RT error rates through sequencing.

Description

Given a samples sheet with some metadata, create a big pile of matrices describing the data.

Usage

create_matrices(
  sample_sheet = "sample_sheets/all_samples.xlsx",
  ident_column = "identtable",
  mut_column = "mutationtable",
  min_reads = NULL,
  min_indexes = NULL,
  min_sequencer = 10,
  min_position = NULL,
  max_position = NULL,
  max_mutations_per_read = NULL,
  prune_n = TRUE,
  excel = NULL,
  verbose = TRUE,
  plot_order = c("dna_control", "dna_low", "dna_high", "rna_control", "rna_low",
    "rna_high"),
  savefile = "sample_tables.rda",
  overwrite = FALSE
)

Arguments

sample_sheet	xlsx/csv/whatever file of metadata.
ident_column	Column containing the files of reads identical to the template.
mut_column	Column containing the files of reads not identical to the template.
min_reads	Filter for the minimum number of reads / index.
min_indexes	Filter for the minimum numer of indexes / mutation.
min_sequencer	Filter defining the minimum number of reads when looking for sequencer-based mutations.
min_position	Filter against weird data at the beginning of the template.
max_position	Filter against weird data at the end.
max_mutations_per_read	Drop reads with more than this number of mutations.
prune_n	Remove mutations which are something to N.
excel	Save data to this file.
verbose	Print information about the running of this function?
plot_order	When plotting, force the order to this.
savefile	Save the timeconsuming portion to this file.
overwrite	If the savefile exists, overwrite it?

Value

List with lots of matrices of the resulting data.

abelew/Rerrrt documentation built on Jan. 15, 2022, 8 a.m.