Filters the regions of a qseaSet using dplyr::filter() predicates
applied to its regions (as a data frame), then subsets the object
accordingly.
filterWindows(qseaSet, ...)qseaSet.
The qseaSet object whose regions (windows) will be filtered.
Expressions.
Predicates passed to dplyr::filter() and evaluated on the regions data
frame.
Default: none (no filtering).
A qseaSet object with only regions matching the filter conditions.
Both the count_matrix and @regions slot are updated consistently.
qsea::getRegions(),
filter.qseaSet() (for filtering samples instead of regions),
dplyr::filter()
data(exampleTumourNormal, package = "mesa")
# Keep regions starting before position 25,020,000
exampleTumourNormal %>% filterWindows(start <= 25020000)
#> qseaSet
#> =======================================
#> 10 Samples:
#> Colon1_N, Colon1_T, Colon2_N, Colon2_T, Lung1_N, Lung1_T, Lung2_N, Lung2_T, Lung3_N, Lung3_T
#> 12 Regions in 22 chromosomes of BSgenome.Hsapiens.NCBI.GRCh38
# Keep regions with CpG density > 10
exampleTumourNormal %>% filterWindows(CpG_density > 10)
#> qseaSet
#> =======================================
#> 10 Samples:
#> Colon1_N, Colon1_T, Colon2_N, Colon2_T, Lung1_N, Lung1_T, Lung2_N, Lung2_T, Lung3_N, Lung3_T
#> 274 Regions in 22 chromosomes of BSgenome.Hsapiens.NCBI.GRCh38
# Combine multiple conditions
exampleTumourNormal %>%
filterWindows(seqnames == "chr7", CpG_density > 5)
#> qseaSet
#> =======================================
#> 10 Samples:
#> Colon1_N, Colon1_T, Colon2_N, Colon2_T, Lung1_N, Lung1_T, Lung2_N, Lung2_T, Lung3_N, Lung3_T
#> 0 Regions in 22 chromosomes of BSgenome.Hsapiens.NCBI.GRCh38