Calculates profile values of a set of tracks over the loci speficied in a BED file. Data points are taken each bin_size base pairs.
Usage
bw_profile(
bwfiles,
bg_bwfiles = NULL,
loci = NULL,
labels = NULL,
mode = "stretch",
bin_size = 100,
upstream = 2500,
downstream = 2500,
middle = NULL,
ignore_strand = FALSE,
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.
- bg_bwfiles
Path or array of paths to the bigWig files to be used as background.
- loci
BED file or GRanges to summarize
- labels
List of names to give to the mcols of the returned GRanges object. If NULL, file names are used.
- mode
How to handle differences in lengths across loci:
stretch: Anchor each locus on both sides.
start: Anchor all loci on start.
end: Anchor all loci on end.
center: Center all loci.
- bin_size
Bin size. Length of bin in base pairs. The lower, the higher the resolution.
- upstream
Number of base pairs to include upstream of loci.
- downstream
Number of base pairs to include downstream of loci.
- middle
Number of base pairs that the middle section has (in stretch mode). If not provided, median length of all loci is used.
- ignore_strand
Whether to use strand information in BED file.
- 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
Whether to use the bigWig values as they are (none - default) or calculate relative enrichment (relative) by dividing values by global average.
Details
Loci are aligned depending on mode parameter:
stretch. Aligns all starts and all ends, sort of stretching the loci. The median of these lenghts is taken as the pseudo-length in order to show a realistic plot when displayed.
start. All loci are aligned by start.
end. All loci are aligned by end.
center. All loci are aligned by center.
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")
# Profiles are returned in long format and include mean, median and stderror
bw_profile(bw, loci = bed, mode = "stretch")
#> mean sderror median index sample
#> 1 2.651766 0.4211416 1.868056 1 sample_H33_ChIP
#> 2 2.353699 0.3952149 1.744718 2 sample_H33_ChIP
#> 3 2.372053 0.4093088 1.675340 3 sample_H33_ChIP
#> 4 2.516681 0.2644566 2.112161 4 sample_H33_ChIP
#> 5 2.288359 0.2839340 1.683047 5 sample_H33_ChIP
#> 6 2.415918 0.3109912 1.837221 6 sample_H33_ChIP
#> 7 2.256240 0.3219986 1.428663 7 sample_H33_ChIP
#> 8 2.446569 0.2598446 2.232930 8 sample_H33_ChIP
#> 9 2.670303 0.2688390 2.307446 9 sample_H33_ChIP
#> 10 2.729953 0.3336880 2.461619 10 sample_H33_ChIP
#> 11 2.589913 0.2979482 2.258625 11 sample_H33_ChIP
#> 12 2.836956 0.3623161 2.669751 12 sample_H33_ChIP
#> 13 2.503650 0.2598396 2.448771 13 sample_H33_ChIP
#> 14 2.965801 0.3900738 2.854759 14 sample_H33_ChIP
#> 15 2.999204 0.4036154 2.507870 15 sample_H33_ChIP
#> 16 3.028204 0.4874518 2.471897 16 sample_H33_ChIP
#> 17 3.386287 0.6245647 2.235501 17 sample_H33_ChIP
#> 18 3.700873 0.7401184 2.556693 18 sample_H33_ChIP
#> 19 3.609102 0.5534036 3.032059 19 sample_H33_ChIP
#> 20 3.701056 0.5778502 3.003792 20 sample_H33_ChIP
#> 21 3.428869 0.5597654 2.405090 21 sample_H33_ChIP
#> 22 3.949016 0.6592606 2.949832 22 sample_H33_ChIP
#> 23 3.247899 0.4771775 2.590096 23 sample_H33_ChIP
#> 24 3.229546 0.4894977 2.058201 24 sample_H33_ChIP
#> 25 3.079227 0.4333806 2.497594 25 sample_H33_ChIP
#> 26 3.639487 0.3295900 3.067325 26 sample_H33_ChIP
#> 27 3.615557 0.3111358 3.394724 27 sample_H33_ChIP
#> 28 3.114177 0.2877722 2.646299 28 sample_H33_ChIP
#> 29 3.087110 0.2202857 2.971876 29 sample_H33_ChIP
#> 30 2.889450 0.2188670 2.972835 30 sample_H33_ChIP
#> 31 2.875842 0.2616709 2.387392 31 sample_H33_ChIP
#> 32 2.929630 0.3522394 2.125642 32 sample_H33_ChIP
#> 33 3.015563 0.3073536 2.458524 33 sample_H33_ChIP
#> 34 3.262732 0.3419128 2.545657 34 sample_H33_ChIP
#> 35 3.247373 0.3754521 2.880982 35 sample_H33_ChIP
#> 36 2.866761 0.3246729 2.409001 36 sample_H33_ChIP
#> 37 3.005472 0.3119875 2.753080 37 sample_H33_ChIP
#> 38 2.837359 0.3052706 2.548127 38 sample_H33_ChIP
#> 39 2.783164 0.2945724 2.463294 39 sample_H33_ChIP
#> 40 2.764363 0.2670326 2.307549 40 sample_H33_ChIP
#> 41 2.304252 0.2265529 2.403486 41 sample_H33_ChIP
#> 42 2.184851 0.2097188 1.877814 42 sample_H33_ChIP
#> 43 2.464733 0.2289928 2.594486 43 sample_H33_ChIP
#> 44 2.691855 0.2693417 2.539616 44 sample_H33_ChIP
#> 45 2.486217 0.2913635 2.108200 45 sample_H33_ChIP
#> 46 2.935590 0.3138470 2.815516 46 sample_H33_ChIP
#> 47 2.968804 0.3694925 2.486643 47 sample_H33_ChIP
#> 48 3.270211 0.4223941 2.603432 48 sample_H33_ChIP
#> 49 3.315354 0.3763270 2.815344 49 sample_H33_ChIP
#> 50 3.184501 0.3060692 2.718847 50 sample_H33_ChIP
#> 51 3.199918 0.3176035 3.066064 51 sample_H33_ChIP
#> 52 3.483032 0.3648622 3.841766 52 sample_H33_ChIP
#> 53 3.384507 0.3127053 3.642152 53 sample_H33_ChIP
#> 54 3.817368 0.3883696 3.355289 54 sample_H33_ChIP
#> 55 3.434996 0.3796849 3.155996 55 sample_H33_ChIP
#> 56 3.562528 0.3944338 3.124369 56 sample_H33_ChIP
#> 57 3.833116 0.4650076 3.173232 57 sample_H33_ChIP
#> 58 3.619649 0.4051178 3.533681 58 sample_H33_ChIP
#> 59 3.932313 0.4788887 3.552670 59 sample_H33_ChIP
#> 60 4.024829 0.4890062 3.387589 60 sample_H33_ChIP
#> 61 3.781616 0.4874027 2.603114 61 sample_H33_ChIP
#> 62 3.744094 0.4913049 3.453766 62 sample_H33_ChIP
#> 63 3.630780 0.4449057 3.087544 63 sample_H33_ChIP
#> 64 4.185833 0.5204512 3.224522 64 sample_H33_ChIP
#> 65 3.549521 0.4470859 2.678337 65 sample_H33_ChIP
#> 66 3.624105 0.4487285 3.117284 66 sample_H33_ChIP
#> 67 4.186247 0.4988139 3.857999 67 sample_H33_ChIP
#> 68 4.398364 0.5437542 3.731710 68 sample_H33_ChIP
#> 69 4.186880 0.5684283 4.162147 69 sample_H33_ChIP
#> 70 4.541604 0.6031076 4.152863 70 sample_H33_ChIP
#> 71 4.882680 0.6583484 3.330124 71 sample_H33_ChIP
#> 72 4.434294 0.6184024 2.805938 72 sample_H33_ChIP
#> 73 4.465311 0.5204311 3.211924 73 sample_H33_ChIP
#> 74 4.586631 0.5179597 3.784932 74 sample_H33_ChIP
#> 75 5.412189 0.6808004 4.478709 75 sample_H33_ChIP
#> 76 5.130822 0.5404398 5.056854 76 sample_H33_ChIP
#> 77 4.772371 0.5835512 3.497144 77 sample_H33_ChIP
#> 78 4.788891 0.5987570 4.242311 78 sample_H33_ChIP
#> 79 4.642610 0.5283055 4.316828 79 sample_H33_ChIP
#> 80 4.774207 0.5970659 4.409330 80 sample_H33_ChIP
#> 81 5.120912 0.7053851 3.702708 81 sample_H33_ChIP
#> 82 4.547538 0.5918970 3.625621 82 sample_H33_ChIP
#> 83 4.387126 0.6446382 3.304428 83 sample_H33_ChIP
#> 84 4.410434 0.5801318 3.330123 84 sample_H33_ChIP
#> 85 4.598745 0.5873002 3.309566 85 sample_H33_ChIP
#> 86 4.879927 0.6950630 2.482175 86 sample_H33_ChIP
#> 87 4.236072 0.5543600 2.795659 87 sample_H33_ChIP
#> 88 4.839732 0.6169402 3.612772 88 sample_H33_ChIP
#> 89 4.661699 0.6013412 2.931846 89 sample_H33_ChIP
#> 90 4.404561 0.5651088 3.810628 90 sample_H33_ChIP
#> 91 4.019680 0.4757994 3.006362 91 sample_H33_ChIP
#> 92 4.426952 0.5882985 4.100985 92 sample_H33_ChIP
#> 93 4.569928 0.5732725 3.224773 93 sample_H33_ChIP
#> 94 4.322334 0.4856785 3.736111 94 sample_H33_ChIP
#> 95 4.874971 0.6007702 3.954522 95 sample_H33_ChIP
bw_profile(bw, loci = bed, mode = "start",
upstream = 1000, downstream = 1500)
#> mean sderror median index sample
#> 1 3.028204 0.4874518 2.471897 1 sample_H33_ChIP
#> 2 3.386287 0.6245647 2.235501 2 sample_H33_ChIP
#> 3 3.700873 0.7401184 2.556693 3 sample_H33_ChIP
#> 4 3.609102 0.5534036 3.032059 4 sample_H33_ChIP
#> 5 3.701056 0.5778502 3.003792 5 sample_H33_ChIP
#> 6 3.428869 0.5597654 2.405090 6 sample_H33_ChIP
#> 7 3.949016 0.6592606 2.949832 7 sample_H33_ChIP
#> 8 3.247899 0.4771775 2.590096 8 sample_H33_ChIP
#> 9 3.229546 0.4894977 2.058201 9 sample_H33_ChIP
#> 10 3.079227 0.4333806 2.497594 10 sample_H33_ChIP
#> 11 3.460437 0.3494176 2.996084 11 sample_H33_ChIP
#> 12 3.469246 0.2405814 2.898442 12 sample_H33_ChIP
#> 13 3.381148 0.3136780 3.032057 13 sample_H33_ChIP
#> 14 3.660127 0.3422368 3.309567 14 sample_H33_ChIP
#> 15 3.733174 0.2724274 3.535686 15 sample_H33_ChIP
#> 16 3.662145 0.3113339 3.353250 16 sample_H33_ChIP
#> 17 3.398767 0.3298550 2.978097 17 sample_H33_ChIP
#> 18 3.589647 0.3335419 3.399501 18 sample_H33_ChIP
#> 19 3.318746 0.3828422 3.006362 19 sample_H33_ChIP
#> 20 3.207521 0.3832718 2.733991 20 sample_H33_ChIP
#> 21 3.188432 0.3926917 2.620930 21 sample_H33_ChIP
#> 22 3.133921 0.3670644 2.649196 22 sample_H33_ChIP
#> 23 2.840810 0.3200884 2.477036 23 sample_H33_ChIP
#> 24 2.856044 0.2712727 2.895871 24 sample_H33_ChIP
#> 25 2.928174 0.2922429 2.644057 25 sample_H33_ChIP