Sort samples in a qseaSet

Extends base::sort() to reorder the samples of a qseaSet using gtools::mixedsort() so that numeric parts sort naturally (e.g., "2" comes before "10").

# S3 method for class 'qseaSet'
sort(x, decreasing = FALSE, ...)

Arguments

x

qseaSet. A qseaSet object to reorder.

decreasing

logical(1). Whether to reverse the order. Default: FALSE.

...

Additional arguments passed on to gtools::mixedsort(). Default: none.

Value

A qseaSet object with reordered samples. The content of all slots (e.g., count_matrix, sampleTable) is updated consistently.

See also

qsea::getSampleNames(), subsetQset(), gtools::mixedsort()

Examples

data(exampleTumourNormal, package = "mesa")

# Sort samples in natural (mixed) order
exampleTumourNormal %>% sort()
#> qseaSet
#> =======================================
#> 10 Samples: 
#> Colon1_N, Colon1_T, Colon2_N, Colon2_T, Lung1_N, Lung1_T, Lung2_N, Lung2_T, Lung3_N, Lung3_T
#> 819 Regions in 22 chromosomes of BSgenome.Hsapiens.NCBI.GRCh38

# Sort in reverse order
exampleTumourNormal %>% sort(decreasing = TRUE)
#> qseaSet
#> =======================================
#> 10 Samples: 
#> Lung3_T, Lung3_N, Lung2_T, Lung2_N, Lung1_T, Lung1_N, Colon2_T, Colon2_N, Colon1_T, Colon1_N
#> 819 Regions in 22 chromosomes of BSgenome.Hsapiens.NCBI.GRCh38