mRSD_check: mRSD checker
In Beirnaert/MetaboMeeseeks: Helper functions for metabolomics analysis

Description Usage Arguments Value Author(s)

mRSD checker

mRSD_check(DataMatrix, subclasses = NULL, labels = NULL,
  RSD_threshold = 0.4, ignore_missing_values = TRUE,
  NA_or_numeric_limit = NA, feature_orientation = "columns",
  groups_ok_threshold = 1, include_RSD_matrix = FALSE)

`DataMatrix`	A matrix with feature groups as columns and samples for rows.
`subclasses`	A vector with characters or factors corresponding to those found in the 'labels' attribute. This can also be a list of vectors in case multiple variables are supplied in the labels parameter.
`labels`	A vector of labels which can be used to group the samples together in subclasses. This attribute is necessary if 'subclasses' is provided. Note this can also be a list in case 2 variables need to be combined for the calculation (for example Batch x sample group). The length of 'labels', or each element in the list has to be the same as the number of rows in the DataMatrix.
`RSD_threshold`	The maximal RSD value (sd/mean) allowed in a single subclass.
`ignore_missing_values`	Whether to ignore the missing values. If set to FALSE the calculation of the RSD will result in a lot of 'NAs' or 'NANs'. Only the features with no missing values will produce a numeric RSD.
`NA_or_numeric_limit`	Define the missing values, this can be set to 'NA' or to a numerical value in which case all values below this value will be deemed missing.
`feature_orientation`	Indicates whether the features can be found in the columns (default) or in the rows. With the default setting every row corresponds to a sample, and every column to a feature/group
`groups_ok_threshold`	The amount of subclasses (as defined in subclasses_list)
`include_RSD_matrix`	If set to 'TRUE' the output will not only be a vector with the indices of groups that passed the RSD check, but also the matrix with all RSD values is provided.

RSD_results A vector with the indices of the groups that passed the test for RSD. If however the 'include_RSD_matrix' attribute is set to 'TRUE' the results will be a list with the vector of indices (list entry 1) and the matrix of RSD for each combination of subclass and feature (list entry 2)

Charlie Beirnaert, charlie.beirnaert@uantwerpen.be

Beirnaert/MetaboMeeseeks documentation built on May 20, 2019, 11:09 a.m.