Construct a multiOmicDataSet object from data frames

Construct a multiOmicDataSet object from data frames

Usage

create_multiOmicDataSet_from_dataframes(
  sample_metadata,
  counts_dat,
  sample_id_colname = NULL,
  feature_id_colname = NULL,
  count_type = "raw"
)

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.

counts_dat

data frame of feature counts (e.g. expected feature counts from RSEM).

sample_id_colname

name of the column in sample_metadata that contains the sample IDs. (Default: NULL - first column in the sample metadata will be used.)

feature_id_colname

name of the column in counts_dat that contains feature/gene IDs. (Default: NULL - first column in the count data will be used.)

count_type

type to assign the values of counts_dat to in the counts slot

Value

A multiOmicDataSet object.

See also

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

Examples

sample_meta_dat <- data.frame(sample_id = c("s1", "s2"), group = c("A", "B"))
feature_counts_dat <- data.frame(
  feature_id = c("gene1", "gene2"),
  s1 = c(10, 20),
  s2 = c(15, 25)
)
moo <- create_multiOmicDataSet_from_dataframes(
  sample_metadata = sample_meta_dat,
  counts_dat = feature_counts_dat
)
head(moo@sample_meta)
#>   sample_id group
#> 1        s1     A
#> 2        s2     B
head(moo@counts[['raw']])
#>   feature_id s1 s2
#> 1      gene1 10 15
#> 2      gene2 20 25