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Re-order samples in a TIRTLseqDataSet object

reorder_samples.Rd

[Experimental] This function changes the order of the samples in a TIRTLseqDataSet object to the order that the user specifies.

Usage

reorder_samples(data, samples)

Arguments

data

a TIRTLseqDataSet object

samples

the samples of 'data', in their desired order.

Either:

  1. A numeric vector of indices

  2. A character vector of sample names

  3. A character vector of metadata conditions where each entry is of the form "column==value"

Value

A TIRTLseqDataSet object with re-ordered samples.

See also

Other data_wrangling: add_metadata(), filter_dataset()

Examples

folder = system.file("extdata/SJTRC_TIRTL_seq_longitudinal",
  package = "TIRTLtools")
sjtrc = load_tirtlseq(folder,
  meta_columns = c("marker", "timepoint", "version"), sep = "_",
  chain = "paired", verbose = FALSE)
print(sjtrc$meta)
#> # A tibble: 6 × 5
#>   sample_id  marker timepoint version label                                     
#>   <chr>      <chr>  <chr>     <chr>   <chr>                                     
#> 1 cd4_tp1_v2 cd4    tp1       v2      marker: cd4 | timepoint: tp1 | version: v2
#> 2 cd4_tp2_v2 cd4    tp2       v2      marker: cd4 | timepoint: tp2 | version: v2
#> 3 cd4_tp3_v2 cd4    tp3       v2      marker: cd4 | timepoint: tp3 | version: v2
#> 4 cd8_tp1_v2 cd8    tp1       v2      marker: cd8 | timepoint: tp1 | version: v2
#> 5 cd8_tp2_v2 cd8    tp2       v2      marker: cd8 | timepoint: tp2 | version: v2
#> 6 cd8_tp3_v2 cd8    tp3       v2      marker: cd8 | timepoint: tp3 | version: v2
new_order = names(sjtrc$data) %>% rev()
print(new_order)
#> [1] "cd8_tp3_v2" "cd8_tp2_v2" "cd8_tp1_v2" "cd4_tp3_v2" "cd4_tp2_v2"
#> [6] "cd4_tp1_v2"
sjtrc = reorder_samples(sjtrc, new_order)
print(sjtrc$meta)
#> # A tibble: 6 × 5
#>   sample_id  marker timepoint version label                                     
#>   <chr>      <chr>  <chr>     <chr>   <chr>                                     
#> 1 cd8_tp3_v2 cd8    tp3       v2      marker: cd8 | timepoint: tp3 | version: v2
#> 2 cd8_tp2_v2 cd8    tp2       v2      marker: cd8 | timepoint: tp2 | version: v2
#> 3 cd8_tp1_v2 cd8    tp1       v2      marker: cd8 | timepoint: tp1 | version: v2
#> 4 cd4_tp3_v2 cd4    tp3       v2      marker: cd4 | timepoint: tp3 | version: v2
#> 5 cd4_tp2_v2 cd4    tp2       v2      marker: cd4 | timepoint: tp2 | version: v2
#> 6 cd4_tp1_v2 cd4    tp1       v2      marker: cd4 | timepoint: tp1 | version: v2