multiOmicDataSet class

multiOmicDataSet class

Usage

multiOmicDataSet(sample_metadata, anno_dat, counts_lst, analyses_lst = list())

Arguments

sample_metadata

sample metadata as a data frame or tibble. The first column is assumed to contain the sample IDs which must correspond to column names in the raw counts.

anno_dat

data frame of feature annotations, such as gene symbols or any other information about the features in counts_lst.

counts_lst

named list of data frames containing counts, e.g. expected feature counts from RSEM. Each data frame is expected to contain a feature_id column as the first column, and all remaining columns are sample IDs in the sample_meta.

analyses_lst

named list of analysis results, e.g. DESeq results object

Value

A multiOmicDataSet S7 object.

See also

Other moo: create_multiOmicDataSet_from_dataframes(), create_multiOmicDataSet_from_files(), extract_counts(), read_multiOmicDataSet(), read_multiOmicDataSet_properties(), write_multiOmicDataSet(), write_multiOmicDataSet_properties()

Additional properties

@sample_meta

sample metadata as a data frame or tibble. The first column is assumed to contain the sample IDs which must correspond to column names in the raw counts.

@counts

named list of counts data frames (e.g. raw, clean, cpm, filt, norm, batch). Each data frame is expected to contain a feature ID column as the first column, and all remaining columns are sample IDs.

@annotation

data frame of feature annotations, such as gene symbols or any other information about the features in the counts list.

@analyses

named list of analysis results (e.g. DESeq2 results, colors).

Examples

# sample metadata (sample names, labels, groups, batches, etc.)
sample_metadata <- data.frame(sample_id = c("s1", "s2"), group = c("A", "B"))
# counts data such as from bulk RNA-seq
counts_dat <- data.frame(
  feature_id = c("gene1", "gene2"),
  s1 = c(10, 20),
  s2 = c(15, 25)
)
# annotations for the counts data such as alternative gene names, gene IDs, etc.
anno_dat <- data.frame(feature_id = c("gene1", "gene2"), ensembl_id = c('ENSG000001', 'ENSG000002'))

# construct a multiOmicDataSet object
moo <- multiOmicDataSet(
  sample_metadata = sample_metadata,
  counts_lst = list(raw = counts_dat),
  anno_dat = anno_dat
)
moo
#> <MOObject::multiOmicDataSet>
#>  @ sample_meta:'data.frame':	2 obs. of  2 variables:
#>  .. $ sample_id: chr  "s1" "s2"
#>  .. $ group    : chr  "A" "B"
#>  @ counts     :List of 1
#>  .. $ raw:'data.frame':	2 obs. of  3 variables:
#>  ..  ..$ feature_id: chr [1:2] "gene1" "gene2"
#>  ..  ..$ s1        : num [1:2] 10 20
#>  ..  ..$ s2        : num [1:2] 15 25
#>  @ annotation :'data.frame':	2 obs. of  2 variables:
#>  .. $ feature_id: chr  "gene1" "gene2"
#>  .. $ ensembl_id: chr  "ENSG000001" "ENSG000002"
#>  @ analyses   : list()
S7::S7_class(moo)
#> <MOObject::multiOmicDataSet> class
#> @ parent     : <S7_object>
#> @ constructor: function(sample_metadata, anno_dat, counts_lst, analyses_lst) {...}
#> @ validator  : function(self) {...}
#> @ properties :
#>  $ sample_meta: S3<data.frame>
#>  $ counts     : <list>        
#>  $ annotation : S3<data.frame>
#>  $ analyses   : <list>        

# validate the object
S7::validate(moo)

# Retrieve properties from the object
head(moo@sample_meta)
#>   sample_id group
#> 1        s1     A
#> 2        s2     B
# Set properties in the object
moo@sample_meta$batch <- c("C", "D")