poplin-combine-slash-subset: Combining or subsetting poplin objects

In jaehyunjoo/poplin: LC/MS Metabolomics Data Processing Utilities

Description

Methods to combine multiple poplin objects by row or column, or to subset a poplin object by row or column.

Combining

In the code snippets below, ... represents multiple poplin objects to be combined.

rbind(..., deparse.level = 1):

Take a sequence of poplin objects in ... and combine by rows. Note that all objects in ... must have the exact same values for poplin_data_list. See ?rbind for the interpretation of deparse.level.

cbind(..., deparse.level = 1):

Take a sequence of poplin objects in ... and combine by columns. Note that all objects in ... must have the same values of poplin_reduced_names. Dimension reduction results with the same name across the objects will be combined row-wise to create the corresponding entry in the output object. See ?cbind for the interpretation of deparse.level.

Refer to help("SummarizedExperiment-class", package = "SummarizedExperiment") for details on how rowData, colData, and metadata are combined in the output object.

Subsetting

In the code snippets below, x is a poplin object.

x[i, j], x[i, j] <- value:

i and j are indices specifying the rows and columns to extract or replace. Indices can be a logical, integer, character vector, or empty (missing). value must be a poplin object with the dimension and assay elements consistent with the subset x[i, j] being replaced. value is also expected to have the same name and order of poplin_data_names (and poplin_reduced_names as well if j is specified) as x.

jaehyunjoo/poplin documentation built on Jan. 8, 2022, 1:13 a.m.