After mapping data to segments, this function can be used to remove segments that are too short, or that have too few mapped RNA genes or ATAC peaks. A parameters allows to input a list of segments that will be retained no matter what.
The function requires and returns an (R)CONGAS+ object.
filter_segments(
x,
length = 0,
RNA_genes = 50,
ATAC_peaks = 50,
segments = list(),
RNA_nonzerocells = 0,
ATAC_nonzerocells = 0
)An rcongasplus object.
Mimium size in number of bases for each segment. This is 0
by default, and therefore non effective.
Required number of RNA genes, if RNA is available. This is
50 by default.
Required number of ATAC peaks, if ATAC is available. This is
50 by default.
A list of segment ids to retain regardless of the filters.
The object x where segments have been identified and
removed.
data('example_object')
# Default
print(example_object)
#> ── [ (R)CONGAS+ ] SU008 TUMOR 30 segments (73.66% genome) ──────────────────────
#>
#> ── CNA segments (reference: GRCh38)
#> → Input 30 CNA segments, mean ploidy 3.2.
#>
#> | | | | | | | | | | | | | | | | | | | |
#>
#> Ploidy: 0 1 2 3 4 5 *
#>
#> ── Modalities
#> → RNA: 714 cells with 8613 mapped genes, 1401728 non-zero values. Likelihood: Negative Binomial.
#> → ATAC: 259 cells with 284316 mapped peaks, 3083691 non-zero values. Likelihood: Negative Binomial.
#> ! Clusters: not available.
#>
#> ── LOG ──
#>
#> - 2021-03-30 17:58:41 Created input object.
#> - 2021-03-30 17:58:43 Filtered outliers: [6|0.05|0.95]
#> [1] 0
example_object %>%
filter_segments() %>%
print()
#> ── Segments filter
#> → 0 retained segments out of 30.
#> Error in filter_segments(.): All segments removed with these parameters.
# Minimum size
example_object %>%
filter_segments(length = 1e7) %>%
print()
#>
#> ── Segments filter
#> → 0 retained segments out of 30.
#> Error in filter_segments(., length = 1e+07): All segments removed with these parameters.