Construct a reneeDataSet object from tsv files.

Usage

create_reneeDataSet_from_files(gene_counts_filepath, sample_meta_filepath)

Arguments

gene_counts_filepath: path to tsv file of expected gene counts from RSEM.
sample_meta_filepath: path to tsv file with sample IDs and metadata for differential analysis.

Value

reneeDataSet object

Examples

create_reneeDataSet_from_files(
  system.file("extdata", "RSEM.genes.expected_count.all_samples.txt", package = "reneeTools"),
  system.file("extdata", "sample_metadata.tsv", package = "reneeTools")
)
#> Rows: 58929 Columns: 6
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (2): gene_id, GeneName
#> dbl (4): KO_S3, KO_S4, WT_S1, WT_S2
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Rows: 4 Columns: 2
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: "\t"
#> chr (2): sample_id, condition
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> <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")=
#>   .. cols(
#>   ..   gene_id = col_character(),
#>   ..   GeneName = col_character(),
#>   ..   KO_S3 = col_double(),
#>   ..   KO_S4 = col_double(),
#>   ..   WT_S1 = col_double(),
#>   ..   WT_S2 = col_double()
#>   .. )
#>  - attr(*, "problems")=<externalptr> 
#>  @ sample_meta:'data.frame':	4 obs. of  1 variable:
#>  .. $ condition: chr  "knockout" "knockout" "wildtype" "wildtype"
#>  @ analyses   : list()