calc_expression_metrics: Quantify expression metrics for qc purposes

In Benjamin-Vincent-Lab/binfotron: Binfotron Bioinformatics Analysis Tools Suite

Quantify expression metrics for qc purposes

Description

Calculates normalization factors used for uq normalization. Also calculates the number of genes that are over min_reads for QC purposes.

Usage

calc_expression_metrics(
  my_dt = NULL,
  col_names = NULL,
  my_summary =
    "Calculating expression normalization factors and % of genes with counts over min_reads for QC.",
  norm_factor = 1000,
  percentile = 75,
  min_reads = c(0, 1, 4),
  sample_key = get_default_sample_key(),
  readme_path = NULL
)

Arguments

my_dt	data.table input
col_names	Vector of character strings to name the columns that will have this operation performed on them. Uses operatable_columns
my_summary	Character string to change the default comment that will be appended to my_dt.
norm_factor	Number indicating the value to which the quartile is normalized
percentile	Percentile to which the data will be normalized
min_reads	Vector of integers for expression to be over to calc percentage of genes over those values
sample_key	Character string to specify the column that is the sample key. This column will not be operated upon.
readme_path	Optional path to which the comments will be appended.

Details

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ calc_expression_metrics ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Benjamin-Vincent-Lab/binfotron documentation built on Oct. 1, 2024, 8:33 p.m.