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Construct a multiOmicDataSet object from data frames

Source: R/0_mo-class.R
create_multiOmicDataSet_from_dataframes.Rd

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

multiOmicDataSet object

See also

Other moo constructors: create_multiOmicDataSet_from_files(), multiOmicDataSet()

Examples

sample_meta <- data.frame(
  sample_id = c("KO_S3", "KO_S4", "WT_S1", "WT_S2"),
  condition = factor(
    c("knockout", "knockout", "wildtype", "wildtype"),
    levels = c("wildtype", "knockout")
  )
)
moo <- create_multiOmicDataSet_from_dataframes(sample_meta, gene_counts)
head(moo@sample_meta)
#>   sample_id condition
#> 1     KO_S3  knockout
#> 2     KO_S4  knockout
#> 3     WT_S1  wildtype
#> 4     WT_S2  wildtype
head(moo@counts$raw)
#> # A tibble: 6 × 5
#>   gene_id            KO_S3 KO_S4 WT_S1 WT_S2
#>   <chr>              <dbl> <dbl> <dbl> <dbl>
#> 1 ENSG00000121410.11     0     0     0     0
#> 2 ENSG00000268895.5      0     0     0     0
#> 3 ENSG00000148584.15     0     0     0     0
#> 4 ENSG00000175899.14     0     0     0     0
#> 5 ENSG00000245105.3      0     0     0     0
#> 6 ENSG00000166535.20     0     0     0     0
head(moo@annotation)
#> # A tibble: 6 × 2
#>   gene_id            GeneName
#>   <chr>              <chr>   
#> 1 ENSG00000121410.11 A1BG    
#> 2 ENSG00000268895.5  A1BG-AS1
#> 3 ENSG00000148584.15 A1CF    
#> 4 ENSG00000175899.14 A2M     
#> 5 ENSG00000245105.3  A2M-AS1 
#> 6 ENSG00000166535.20 A2ML1