Build a scored GRanges object from a bigWig file list and a BED file or GRanges object. The aggregating function (per locus) can be min, max, sd, mean.
Usage
bw_loci(
bwfiles,
loci,
bg_bwfiles = NULL,
labels = NULL,
per_locus_stat = "mean",
aggregate_by = NULL,
norm_mode = "fc",
remove_top = 0,
default_na = NA_real_,
scaling = "none"
)Arguments
- bwfiles
Path or array of paths to the bigWig files to be summarized.
- loci
GRanges or BED file to summarize the BigWig file at.
- bg_bwfiles
Path or array of paths to the bigWig files to be used as background.
- labels
List of names to give to the mcols of the returned GRanges object. If NULL, file names are used.
- per_locus_stat
Aggregating function (per locus). Mean by default. Choices: min, max, sd, mean.
- aggregate_by
Statistic to aggregate per group. If NULL, values are not aggregated. This is the behavior by default.
- norm_mode
Function to apply to normalize bin values. Default fc: divides bw / bg. Alternative: log2fc: returns log2(bw/bg).
- remove_top
Return range 0-(1-remove_top). By default returns the whole distribution (remove_top == 0).
- default_na
Default value for missing values
- scaling
If none, no operation is performed (default). If relative, values are divided by global mean (1x genome coverage).
Value
A GRanges object with each bwfile as a metadata column named after labels, if provided, or after filenames otherwise.
Details
Values can be normalized using background bigWig files (usually input files). By default, the value obtained will be bigwig / bg_bigwig per locus, per bigWig.
bwfiles and bg_bwfiles must have the same length. If you are using same background for several files, then file paths must be repeated accordingly.
norm_mode can be either "fc", where values will represent bigwig / bg_bigwig, or "log2fc", values will represent log2(bigwig / bg_bigwig) per locus.
Examples
# Get the raw files
bed <- system.file("extdata", "sample_genes_mm9.bed", package="wigglescout")
bw <- system.file("extdata", "sample_H33_ChIP.bw", package="wigglescout")
bw2 <- system.file("extdata",
"sample_H3K9me3_ChIP.bw", package="wigglescout")
bw_inp <- system.file("extdata", "sample_Input.bw", package="wigglescout")
# Run single bw with single bed
bw_loci(bw, bed)
#> GRanges object with 26 ranges and 2 metadata columns:
#> seqnames ranges strand | sample_H33_ChIP name
#> <Rle> <IRanges> <Rle> | <numeric> <character>
#> [1] chr15 102751562-102759245 + | 2.91694 Hoxc13
#> [2] chr15 102767284-102768948 + | 3.61492 Hoxc12
#> [3] chr15 102774493-102778377 - | 3.97043 Hotair
#> [4] chr15 102784957-102787132 + | 2.17507 Hoxc11
#> [5] chr15 102797227-102802328 + | 1.45977 Hoxc10
#> ... ... ... ... . ... ...
#> [22] chr15 103078643-103082118 - | 5.51339 Nfe2
#> [23] chr15 103078643-103083241 - | 5.49223 Nfe2
#> [24] chr15 103078643-103083583 - | 5.45826 Nfe2
#> [25] chr15 103078643-103085870 - | 4.87355 Nfe2
#> [26] chr15 103078643-103088834 - | 4.42227 Nfe2
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
# Use of some parameters
bw_loci(bw, bed, labels = c("H33"), remove_top = 0.01)
#> GRanges object with 25 ranges and 2 metadata columns:
#> seqnames ranges strand | H33 name
#> <Rle> <IRanges> <Rle> | <numeric> <character>
#> [1] chr15 102751562-102759245 + | 2.91694 Hoxc13
#> [2] chr15 102767284-102768948 + | 3.61492 Hoxc12
#> [3] chr15 102774493-102778377 - | 3.97043 Hotair
#> [4] chr15 102784957-102787132 + | 2.17507 Hoxc11
#> [5] chr15 102797227-102802328 + | 1.45977 Hoxc10
#> ... ... ... ... . ... ...
#> [21] chr15 103078643-103082118 - | 5.51339 Nfe2
#> [22] chr15 103078643-103083241 - | 5.49223 Nfe2
#> [23] chr15 103078643-103083583 - | 5.45826 Nfe2
#> [24] chr15 103078643-103085870 - | 4.87355 Nfe2
#> [25] chr15 103078643-103088834 - | 4.42227 Nfe2
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
# Log2 fold change
bw_loci(bw, loci = bed, bg_bwfiles = bw_inp, norm_mode = "log2fc")
#> GRanges object with 26 ranges and 2 metadata columns:
#> seqnames ranges strand | sample_H33_ChIP name
#> <Rle> <IRanges> <Rle> | <numeric> <character>
#> [1] chr15 102751562-102759245 + | 1.560373 Hoxc13
#> [2] chr15 102767284-102768948 + | 1.739607 Hoxc12
#> [3] chr15 102774493-102778377 - | 1.805667 Hotair
#> [4] chr15 102784957-102787132 + | 0.954433 Hoxc11
#> [5] chr15 102797227-102802328 + | 0.444870 Hoxc10
#> ... ... ... ... . ... ...
#> [22] chr15 103078643-103082118 - | 2.16692 Nfe2
#> [23] chr15 103078643-103083241 - | 2.13467 Nfe2
#> [24] chr15 103078643-103083583 - | 2.12414 Nfe2
#> [25] chr15 103078643-103085870 - | 1.98608 Nfe2
#> [26] chr15 103078643-103088834 - | 1.87849 Nfe2
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
# Multiple bigWig
bw_loci(c(bw, bw2),
loci = bed,
bg_bwfiles = c(bw_inp, bw_inp),
norm_mode = "log2fc")
#> GRanges object with 26 ranges and 3 metadata columns:
#> seqnames ranges strand | sample_H33_ChIP
#> <Rle> <IRanges> <Rle> | <numeric>
#> [1] chr15 102751562-102759245 + | 1.560373
#> [2] chr15 102767284-102768948 + | 1.739607
#> [3] chr15 102774493-102778377 - | 1.805667
#> [4] chr15 102784957-102787132 + | 0.954433
#> [5] chr15 102797227-102802328 + | 0.444870
#> ... ... ... ... . ...
#> [22] chr15 103078643-103082118 - | 2.16692
#> [23] chr15 103078643-103083241 - | 2.13467
#> [24] chr15 103078643-103083583 - | 2.12414
#> [25] chr15 103078643-103085870 - | 1.98608
#> [26] chr15 103078643-103088834 - | 1.87849
#> sample_H3K9me3_ChIP name
#> <numeric> <character>
#> [1] -4.22203 Hoxc13
#> [2] -3.47525 Hoxc12
#> [3] -4.95146 Hotair
#> [4] -3.88646 Hoxc11
#> [5] -2.60497 Hoxc10
#> ... ... ...
#> [22] -3.58945 Nfe2
#> [23] -3.63653 Nfe2
#> [24] -3.61106 Nfe2
#> [25] -2.94153 Nfe2
#> [26] -3.02280 Nfe2
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths