Construct a multiOmicDataSet object from text files (e.g. TSV, CSV).

Construct a multiOmicDataSet object from text files (e.g. TSV, CSV).

Usage

create_multiOmicDataSet_from_files(
  sample_meta_filepath,
  feature_counts_filepath,
  count_type = "raw",
  sample_id_colname = NULL,
  feature_id_colname = NULL,
  delim = NULL,
  ...
)

Arguments

sample_meta_filepath

path to text file with sample IDs and metadata for differential analysis.

feature_counts_filepath

path to text file of expected feature counts (e.g. gene counts from RSEM).

count_type

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

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.)

delim

Delimiter used in the input files. Any delimiter accepted by readr::read_delim() can be used. If the files are in CSV format, set delim = ','; for TSV format, set delim = '\t'.

...

additional arguments forwarded to readr::read_delim().

Value

A multiOmicDataSet object.

See also

Other moo: create_multiOmicDataSet_from_dataframes(), 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)
)
sample_meta_filepath <- tempfile(fileext = ".csv")
feature_counts_filepath <- tempfile(fileext = ".csv")
readr::write_csv(sample_meta_dat, sample_meta_filepath)
readr::write_csv(feature_counts_dat, feature_counts_filepath)

moo <- create_multiOmicDataSet_from_files(
  sample_meta_filepath = sample_meta_filepath,
  feature_counts_filepath = feature_counts_filepath,
  delim = ","
)
#> Rows: 2 Columns: 3
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr (1): feature_id
#> dbl (2): s1, 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: 2 Columns: 2
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr (2): sample_id, group
#> 
#> 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.
head(moo@sample_meta)
#> # A tibble: 2 × 2
#>   sample_id group
#>   <chr>     <chr>
#> 1 s1        A    
#> 2 s2        B    
head(moo@counts[['raw']])
#> # A tibble: 2 × 3
#>   feature_id    s1    s2
#>   <chr>      <dbl> <dbl>
#> 1 gene1         10    15
#> 2 gene2         20    25