LCD_complex_cutoff: LCD with a signature-specific cutoff on exposures

Description Usage Arguments Value See Also Examples

View source: R/LCD.R

Description

LCD_cutoff performs a mutational signatures decomposition by Linear Combination Decomposition (LCD) of a given mutational catalogue V with known signatures W by solving the minimization problem min(||W*H - V||) with additional constraints of non-negativity on H where W and V are known, but excludes signatures with an overall contribution less than a given signature-specific cutoff (and thereby accounting for a background model) over the whole cohort.

LCD_complex_cutoff_perPID is a wrapper for LCD_complex_cutoff and runs individually for every PID.

Usage

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LCD_complex_cutoff(in_mutation_catalogue_df, in_signatures_df,
  in_cutoff_vector = NULL, in_filename = NULL, in_method = "abs",
  in_per_sample_cutoff = 0, in_rescale = TRUE, in_sig_ind_df = NULL,
  in_cat_list = NULL)

LCD_complex_cutoff_perPID(in_mutation_catalogue_df, in_signatures_df,
  in_cutoff_vector = NULL, in_filename = NULL, in_method = "abs",
  in_rescale = TRUE, in_sig_ind_df = NULL, in_cat_list = NULL)

Arguments

in_mutation_catalogue_df

A numeric data frame V with n rows and m columns, n being the number of features and m being the number of samples

in_signatures_df

A numeric data frame W with n rows and l columns, n being the number of features and l being the number of signatures

in_cutoff_vector

A numeric vector of values less than 1. Signatures from within W with an overall exposure less than the respective value in in_cutoff_vector will be discarded.

in_filename

A path to generate a histogram of the signature exposures if non-NULL

in_method

Indicate to which data the cutoff shall be applied: absolute exposures, relative exposures

in_per_sample_cutoff

A numeric value less than 1. Signatures from within W with an exposure per sample less than in_cutoff will be discarded.

in_rescale

Boolean, if TRUE (default) the exposures are rescaled such that colSums over exposures match colSums over mutational catalogue

in_sig_ind_df

Data frame of type signature_indices_df, i.e. indicating name, function and meta-information of the signatures. Default is NULL.

in_cat_list

List of categories for aggregation. Have to be among the column names of in_sig_ind_df. Default is NULL.

Value

A list with entries:

See Also

LCD

aggregate_exposures_by_category

lsei

Examples

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huebschm/YAPSA documentation built on May 17, 2019, 9:11 p.m.