Filter samples in a qseaSet

Extends dplyr::filter() to subset samples in a qseaSet based on predicates applied to its sampleTable.

# S3 method for class 'qseaSet'
filter(.data, ..., .preserve = FALSE)

Arguments

.data

qseaSet A qseaSet object whose samples are to be filtered.

...

Predicate expressions passed to dplyr::filter(), evaluated on the sampleTable. For example, age > 65, tissue == "Colon". Default: none (no filtering).

.preserve

logical(1) Placeholder argument for compatibility with dplyr::filter(). Ignored here since grouping is not implemented. Default: FALSE.

Value

A qseaSet object containing only the samples whose sampleTable rows satisfied the filter expressions. If no samples remain, an empty qseaSet is returned (with a message but not an error).

Details

Filtering is performed on the result of qsea::getSampleTable(.data). Matching rows determine the sample_names retained in the qseaSet. Grouped filtering (group_by) is not supported for qseaSet.

See also

qsea::getSampleTable() to inspect metadata, subsetQset() for explicit sample subsetting, selectQset() for column selection in the sampleTable.

Examples

data(exampleTumourNormal, package = "mesa")

# Keep only older patients
exampleTumourNormal %>% filter(age >= 70)
#> qseaSet
#> =======================================
#> 6 Samples: 
#> Colon1_N, Colon1_T, Lung2_N, Lung2_T, Lung3_N, Lung3_T
#> 819 Regions in 22 chromosomes of BSgenome.Hsapiens.NCBI.GRCh38

# Restrict to colon tissue
exampleTumourNormal %>% filter(tissue == "Colon")
#> qseaSet
#> =======================================
#> 4 Samples: 
#> Colon1_N, Colon1_T, Colon2_N, Colon2_T
#> 819 Regions in 22 chromosomes of BSgenome.Hsapiens.NCBI.GRCh38

# Select only tumour samples
exampleTumourNormal %>% filter(tumour != "Normal")
#> qseaSet
#> =======================================
#> 5 Samples: 
#> Colon1_T, Colon2_T, Lung1_T, Lung2_T, Lung3_T
#> 819 Regions in 22 chromosomes of BSgenome.Hsapiens.NCBI.GRCh38

# Combine predicates: lung tumours only
exampleTumourNormal %>%
    filter(stringr::str_detect(sample_name, "Lung"), tumour != "Normal")
#> qseaSet
#> =======================================
#> 3 Samples: 
#> Lung1_T, Lung2_T, Lung3_T
#> 819 Regions in 22 chromosomes of BSgenome.Hsapiens.NCBI.GRCh38

# If no rows match, returns empty qseaSet (with a message)
exampleTumourNormal %>% filter(tissue == "Liver")
#> No samples remaining, returning an empty qseaSet.
#> qseaSet
#> =======================================
#> 0 Samples: 
#> 
#> 819 Regions in 22 chromosomes of BSgenome.Hsapiens.NCBI.GRCh38