Construct a reneeDataSet object from data frames

Usage

create_reneeDataSet_from_dataframes(count_dat, sample_meta_dat)

Arguments

count_dat: expected gene counts from RSEM as a data frame or tibble. Must contain a gene_id column and a column for each sample ID in the metadata.
sample_meta_dat: sample metadata as a data frame or tibble. Must contain a sample_ID column.

Value

reneeDataSet object

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")
  )
)
create_reneeDataSet_from_dataframes(gene_counts, sample_meta)
#> <renee>
#>  @ counts     : spc_tbl_ [58,929 × 6] (S3: spec_tbl_df/tbl_df/tbl/data.frame)
#>  $ gene_id : chr [1:58929] "ENSG00000121410.11" "ENSG00000268895.5" "ENSG00000148584.15" "ENSG00000175899.14" ...
#>  $ GeneName: chr [1:58929] "A1BG" "A1BG-AS1" "A1CF" "A2M" ...
#>  $ KO_S3   : num [1:58929] 0 0 0 0 0 0 0 0 0 0 ...
#>  $ KO_S4   : num [1:58929] 0 0 0 0 0 0 0 0 0 0 ...
#>  $ WT_S1   : num [1:58929] 0 0 0 0 0 0 0 0 0 0 ...
#>  $ WT_S2   : num [1:58929] 0 0 0 0 0 0 0 0 0 0 ...
#>  - attr(*, "spec")=List of 3
#>   ..$ cols   :List of 6
#>   .. ..$ gene_id : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_character" "collector"
#>   .. ..$ GeneName: list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_character" "collector"
#>   .. ..$ KO_S3   : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_double" "collector"
#>   .. ..$ KO_S4   : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_double" "collector"
#>   .. ..$ WT_S1   : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_double" "collector"
#>   .. ..$ WT_S2   : list()
#>   .. .. ..- attr(*, "class")= chr [1:2] "collector_double" "collector"
#>   ..$ default: list()
#>   .. ..- attr(*, "class")= chr [1:2] "collector_guess" "collector"
#>   ..$ delim  : chr "\t"
#>   ..- attr(*, "class")= chr "col_spec"
#>  - attr(*, "problems")=<externalptr> 
#>  @ sample_meta:'data.frame':	4 obs. of  1 variable:
#>  .. $ condition: Factor w/ 2 levels "wildtype","knockout": 2 2 1 1
#>  @ analyses   : list()