Merge overlapping windows using p-values from significance testing
mergeBySig(x, ...)
# S4 method for class 'GenomicRanges'
mergeBySig(
x,
df = NULL,
logfc = "logFC",
pval = "P",
cpm = "logCPM",
inc_cols,
p_adj_method = "fdr",
alpha = 0.05,
method = c("combine", "best", "minimal"),
merge_within = 1L,
ignore_strand = TRUE,
min_win = 1,
...
)
# S4 method for class 'RangedSummarizedExperiment'
mergeBySig(
x,
df = NULL,
logfc = "logFC",
pval = "P",
cpm = "logCPM",
inc_cols,
p_adj_method = "fdr",
alpha = 0.05,
method = c("combine", "best", "minimal"),
merge_within = 1L,
ignore_strand = TRUE,
...
)GenomicRanges object
Passed to all csaw functions being wrapped
data.frame with results of differential binding analysis performed
using a sliding window strategy. If not provided, the columns in the
mcols() element of x will be used
Column names for the values holding window specific estimates of change in binding (logfc), overall signal intensity (cpm) and the significance from statistical testing (pval)
(Optional) Character vector of any additional columns in
df to return
One of p.adjust.methods
Significance threshold to apply during internal calculations
Shorthand versions for which csaw strategy to use for
merging windows. Choose from 'combine' (combineTests), 'best'
(getBestTest) or 'minimal' (minimalTests).
Merge any non-overlapping windows within this distance
Passed internally to reduce and findOverlaps
Only keep merged windows derived from at least this number
A GenomicRanges object with overlapping ranges from the original object merged and representative values returned. The range corresponding to the representative values is also returned
When using sliding windows to test for differential signal, overlapping
windows can be merged based on the significance of results.
mergeBySig() is a wrapper to the functions combineTests,
getBestTest and minimalTests, using each
function's approach to finding a representative window. The returned object
differs from those returned by the original functions in that the
description of windows as 'up', 'down' or mixed is omitted and the genomic
range corresponding to the representative window is also returned. Column
names also correspond to those in the original object.
An additional column with adjusted p-values is returned. This column retains the same name as the original but with the suffix '_*' added where the p-value adjustment method is added after the underscore.
x <- GRanges(c("chr1:1-10", "chr1:6-15", "chr1:51-60"))
set.seed(1001)
df <- DataFrame(logFC = rnorm(3), logCPM = rnorm(3,8), p = rexp(3, 10))
mcols(x) <- df
mergeBySig(x, pval = "p", method = "combine")
#> GRanges object with 2 ranges and 8 metadata columns:
#> seqnames ranges strand | n_windows n_up n_down keyval_range
#> <Rle> <IRanges> <Rle> | <integer> <integer> <integer> <GRanges>
#> [1] chr1 1-15 * | 2 1 1 chr1:1-10
#> [2] chr1 51-60 * | 1 0 0 chr1:51-60
#> logCPM logFC p p_fdr
#> <numeric> <numeric> <numeric> <numeric>
#> [1] 5.49346 2.188648 0.0184835 0.036967
#> [2] 7.85644 -0.185275 0.3201591 0.320159
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
mergeBySig(x, pval = "p", method = "best")
#> GRanges object with 2 ranges and 8 metadata columns:
#> seqnames ranges strand | n_windows n_up n_down keyval_range
#> <Rle> <IRanges> <Rle> | <integer> <integer> <integer> <GRanges>
#> [1] chr1 1-15 * | 2 1 1 chr1:6-15
#> [2] chr1 51-60 * | 1 0 0 chr1:51-60
#> logCPM logFC p p_fdr
#> <numeric> <numeric> <numeric> <numeric>
#> [1] 7.44269 -0.177547 0.0252419 0.0504838
#> [2] 7.85644 -0.185275 0.3201591 0.3201591
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
mergeBySig(x, pval = "p", method = "min")
#> GRanges object with 2 ranges and 8 metadata columns:
#> seqnames ranges strand | n_windows n_up n_down keyval_range
#> <Rle> <IRanges> <Rle> | <integer> <integer> <integer> <GRanges>
#> [1] chr1 1-15 * | 2 1 1 chr1:1-10
#> [2] chr1 51-60 * | 1 0 0 chr1:51-60
#> logCPM logFC p p_fdr
#> <numeric> <numeric> <numeric> <numeric>
#> [1] 5.49346 2.188648 0.0252419 0.0504838
#> [2] 7.85644 -0.185275 0.3201591 0.3201591
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths