Get dataframe with bootstrapped motif-summit distances
Source:R/get_df_distances_bootstrapped.R
get_df_distances_bootstrapped.RdWrapper for `MotifPeeker::bootstrap_distances` to get bootstrapped
motif-summit distances for given peaks and motifs, generating a
data.frame suitable for plots.
Arguments
- result
A
listwith the following elements:- peaks
A
listof peak files generated usingread_peak_file.- alignments
A
listof alignment files.- exp_type
A
charactervector of experiment types.- exp_labels
A
charactervector of experiment labels.- read_count
A
numericvector of read counts.- peak_count
A
numericvector of peak counts.
- user_motifs
A
listwith the following elements:- motifs
A
listof motif files.- motif_labels
A
charactervector of motif labels.
- genome_build
A character string with the abbreviated genome build name, or a BSGenome object. Check check_genome_build details for genome builds which can be imported as abbreviated names.
- samples_n
An integer specifying the number of bootstrap samples to generate. If
NULL, it is set to 70% of the number of peaks.- samples_len
An integer specifying the number of peaks to sample in each bootstrap iteration. If
NULL, it is set to 20 peaks.- out_dir
A
charactervector of output directory.- BPPARAM
A
BiocParallelParam-classobject enabling parallel execution. (default = SerialParam(), single-CPU run)
Following are two examples of how to set up parallel processing:BPPARAM = BiocParallel::MulticoreParam(4): Uses 4 CPU cores for parallel processing.library("BiocParallel")followed byregister(MulticoreParam(4))sets all subsequent BiocParallel functions to use 4 CPU cores.Motifpeeker()must be run withBPPARAM = BiocParallel::MulticoreParam().
IMPORTANT: For each worker, please ensure a minimum of 8GB of memory (RAM) is available as
motif_discoveryis memory-intensive.- meme_path
path to
meme/bin/(optional). Defaut:NULL, searches "MEME_PATH" environment variable or "meme_path" option for path to "meme/bin/".- verbose
A logical indicating whether to print verbose messages while running the function. (default = FALSE)
Value
A data.frame with the following columns:
- exp_label
Experiment labels.
- exp_type
Experiment types.
- motif_indice
Motif indices.
- bootstrap_iteration
Bootstrap iteration number.
- distance
Mean of absolute distances between peak summit and motif.
See also
Other generate data.frames:
get_df_distances(),
get_df_enrichment()
Examples
if (memes::meme_is_installed()) {
peak <- system.file("extdata", "CTCF_ChIP_peaks.narrowPeak",
package = "MotifPeeker") |>
read_peak_file() |>
sample(20)
motif_MA1102.3 <- system.file("extdata", "motif_MA1102.3.jaspar",
package = "MotifPeeker") |> read_motif_file()
motif_MA1930.2 <- system.file("extdata", "motif_MA1930.2.jaspar",
package = "MotifPeeker") |> read_motif_file()
input <- list(
peaks = peak,
exp_type = "ChIP",
exp_labels = "CTCF",
read_count = 150,
peak_count = 100
)
motifs <- list(
motifs = list(motif_MA1930.2, motif_MA1102.3),
motif_labels = list("MA1930.2", "MA1102.3")
)
if (requireNamespace("BSgenome.Hsapiens.UCSC.hg38")) {
genome_build <-
BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38
distances_df_bootstrapped <- get_df_distances_bootstrapped(
input,
user_motifs = motifs,
genome_build = genome_build,
samples_n = NULL,
samples_len = NULL,
verbose = FALSE
)
print(distances_df_bootstrapped)
}
}
#> exp_label exp_type motif_indice bootstrap_iteration distance
#> 1 CTCF ChIP 1 1 16.800000
#> 2 CTCF ChIP 1 2 27.000000
#> 3 CTCF ChIP 1 3 25.200000
#> 4 CTCF ChIP 1 4 21.500000
#> 5 CTCF ChIP 1 5 14.500000
#> 6 CTCF ChIP 1 6 6.000000
#> 7 CTCF ChIP 1 7 13.500000
#> 8 CTCF ChIP 1 8 12.714286
#> 9 CTCF ChIP 1 9 20.500000
#> 10 CTCF ChIP 1 10 7.000000
#> 11 CTCF ChIP 1 11 10.666667
#> 12 CTCF ChIP 1 12 21.400000
#> 13 CTCF ChIP 1 13 15.200000
#> 14 CTCF ChIP 1 14 6.000000
#> 15 CTCF ChIP 1 15 20.800000
#> 16 CTCF ChIP 1 16 23.200000
#> 17 CTCF ChIP 1 17 20.166667
#> 18 CTCF ChIP 1 18 23.500000
#> 19 CTCF ChIP 1 19 10.666667
#> 20 CTCF ChIP 1 20 13.000000
#> 21 CTCF ChIP 1 21 20.000000
#> 22 CTCF ChIP 1 22 26.800000
#> 23 CTCF ChIP 1 23 15.200000
#> 24 CTCF ChIP 1 24 17.250000
#> 25 CTCF ChIP 1 25 20.000000
#> 26 CTCF ChIP 1 26 16.750000
#> 27 CTCF ChIP 1 27 18.142857
#> 28 CTCF ChIP 1 28 13.666667
#> 29 CTCF ChIP 1 29 38.000000
#> 30 CTCF ChIP 1 30 12.600000
#> 31 CTCF ChIP 1 31 24.166667
#> 32 CTCF ChIP 1 32 15.000000
#> 33 CTCF ChIP 1 33 24.000000
#> 34 CTCF ChIP 1 34 18.000000
#> 35 CTCF ChIP 1 35 19.000000
#> 36 CTCF ChIP 1 36 19.250000
#> 37 CTCF ChIP 1 37 16.800000
#> 38 CTCF ChIP 1 38 7.000000
#> 39 CTCF ChIP 1 39 24.000000
#> 40 CTCF ChIP 1 40 24.166667
#> 41 CTCF ChIP 1 41 18.000000
#> 42 CTCF ChIP 1 42 15.000000
#> 43 CTCF ChIP 1 43 21.833333
#> 44 CTCF ChIP 1 44 23.000000
#> 45 CTCF ChIP 1 45 13.000000
#> 46 CTCF ChIP 1 46 7.000000
#> 47 CTCF ChIP 1 47 20.000000
#> 48 CTCF ChIP 1 48 10.250000
#> 49 CTCF ChIP 1 49 15.200000
#> 50 CTCF ChIP 1 50 20.166667
#> 51 CTCF ChIP 1 51 22.500000
#> 52 CTCF ChIP 1 52 23.333333
#> 53 CTCF ChIP 1 53 13.750000
#> 54 CTCF ChIP 1 54 23.000000
#> 55 CTCF ChIP 1 55 20.200000
#> 56 CTCF ChIP 1 56 19.333333
#> 57 CTCF ChIP 1 57 9.750000
#> 58 CTCF ChIP 1 58 6.666667
#> 59 CTCF ChIP 1 59 28.333333
#> 60 CTCF ChIP 1 60 13.000000
#> 61 CTCF ChIP 1 61 14.600000
#> 62 CTCF ChIP 1 62 21.428571
#> 63 CTCF ChIP 1 63 24.800000
#> 64 CTCF ChIP 1 64 24.000000
#> 65 CTCF ChIP 1 65 25.200000
#> 66 CTCF ChIP 1 66 24.000000
#> 67 CTCF ChIP 1 67 28.333333
#> 68 CTCF ChIP 1 68 25.500000
#> 69 CTCF ChIP 1 69 14.000000
#> 70 CTCF ChIP 1 70 13.000000
#> 71 CTCF ChIP 1 71 16.666667
#> 72 CTCF ChIP 1 72 13.750000
#> 73 CTCF ChIP 1 73 25.571429
#> 74 CTCF ChIP 1 74 9.500000
#> 75 CTCF ChIP 1 75 24.166667
#> 76 CTCF ChIP 1 76 16.500000
#> 77 CTCF ChIP 1 77 13.750000
#> 78 CTCF ChIP 1 78 19.625000
#> 79 CTCF ChIP 1 79 13.750000
#> 80 CTCF ChIP 1 80 28.333333
#> 81 CTCF ChIP 1 81 20.333333
#> 82 CTCF ChIP 1 82 25.500000
#> 83 CTCF ChIP 1 83 19.750000
#> 84 CTCF ChIP 1 84 19.250000
#> 85 CTCF ChIP 1 85 14.000000
#> 86 CTCF ChIP 1 86 20.000000
#> 87 CTCF ChIP 1 87 6.000000
#> 88 CTCF ChIP 1 88 16.666667
#> 89 CTCF ChIP 1 89 26.500000
#> 90 CTCF ChIP 1 90 19.333333
#> 91 CTCF ChIP 1 91 25.200000
#> 92 CTCF ChIP 1 92 20.600000
#> 93 CTCF ChIP 1 93 6.333333
#> 94 CTCF ChIP 1 94 27.000000
#> 95 CTCF ChIP 1 95 20.000000
#> 96 CTCF ChIP 1 96 20.000000
#> 97 CTCF ChIP 1 97 19.000000
#> 98 CTCF ChIP 1 98 12.000000
#> 99 CTCF ChIP 1 99 25.200000
#> 100 CTCF ChIP 1 100 22.500000
#> 101 CTCF ChIP 2 1 16.500000
#> 102 CTCF ChIP 2 2 126.500000
#> 103 CTCF ChIP 2 3 126.500000
#> 104 CTCF ChIP 2 4 126.500000
#> 105 CTCF ChIP 2 5 99.500000
#> 106 CTCF ChIP 2 6 16.500000
#> 107 CTCF ChIP 2 7 70.166667
#> 108 CTCF ChIP 2 8 16.500000
#> 109 CTCF ChIP 2 9 126.500000
#> 110 CTCF ChIP 2 10 16.500000
#> 111 CTCF ChIP 2 11 126.500000
#> 112 CTCF ChIP 2 12 99.500000
#> 113 CTCF ChIP 2 13 NA
#> 114 CTCF ChIP 2 14 16.500000
#> 115 CTCF ChIP 2 15 NA
#> 116 CTCF ChIP 2 16 70.166667
#> 117 CTCF ChIP 2 17 NA
#> 118 CTCF ChIP 2 18 NA
#> 119 CTCF ChIP 2 19 25.000000
#> 120 CTCF ChIP 2 20 NA
#> 121 CTCF ChIP 2 21 16.500000
#> 122 CTCF ChIP 2 22 71.500000
#> 123 CTCF ChIP 2 23 58.833333
#> 124 CTCF ChIP 2 24 44.500000
#> 125 CTCF ChIP 2 25 11.500000
#> 126 CTCF ChIP 2 26 71.500000
#> 127 CTCF ChIP 2 27 14.000000
#> 128 CTCF ChIP 2 28 16.500000
#> 129 CTCF ChIP 2 29 126.500000
#> 130 CTCF ChIP 2 30 14.000000
#> 131 CTCF ChIP 2 31 71.500000
#> 132 CTCF ChIP 2 32 33.500000
#> 133 CTCF ChIP 2 33 51.500000
#> 134 CTCF ChIP 2 34 16.500000
#> 135 CTCF ChIP 2 35 16.500000
#> 136 CTCF ChIP 2 36 NA
#> 137 CTCF ChIP 2 37 51.500000
#> 138 CTCF ChIP 2 38 126.500000
#> 139 CTCF ChIP 2 39 126.500000
#> 140 CTCF ChIP 2 40 71.500000
#> 141 CTCF ChIP 2 41 33.500000
#> 142 CTCF ChIP 2 42 56.750000
#> 143 CTCF ChIP 2 43 37.166667
#> 144 CTCF ChIP 2 44 71.833333
#> 145 CTCF ChIP 2 45 126.500000
#> 146 CTCF ChIP 2 46 16.500000
#> 147 CTCF ChIP 2 47 16.500000
#> 148 CTCF ChIP 2 48 16.500000
#> 149 CTCF ChIP 2 49 70.166667
#> 150 CTCF ChIP 2 50 71.500000
#> 151 CTCF ChIP 2 51 72.500000
#> 152 CTCF ChIP 2 52 53.000000
#> 153 CTCF ChIP 2 53 71.500000
#> 154 CTCF ChIP 2 54 71.500000
#> 155 CTCF ChIP 2 55 NA
#> 156 CTCF ChIP 2 56 16.500000
#> 157 CTCF ChIP 2 57 NA
#> 158 CTCF ChIP 2 58 NA
#> 159 CTCF ChIP 2 59 14.000000
#> 160 CTCF ChIP 2 60 126.500000
#> 161 CTCF ChIP 2 61 33.500000
#> 162 CTCF ChIP 2 62 99.500000
#> 163 CTCF ChIP 2 63 42.000000
#> 164 CTCF ChIP 2 64 NA
#> 165 CTCF ChIP 2 65 11.166667
#> 166 CTCF ChIP 2 66 NA
#> 167 CTCF ChIP 2 67 71.500000
#> 168 CTCF ChIP 2 68 44.500000
#> 169 CTCF ChIP 2 69 126.500000
#> 170 CTCF ChIP 2 70 16.500000
#> 171 CTCF ChIP 2 71 16.500000
#> 172 CTCF ChIP 2 72 53.000000
#> 173 CTCF ChIP 2 73 71.500000
#> 174 CTCF ChIP 2 74 NA
#> 175 CTCF ChIP 2 75 16.500000
#> 176 CTCF ChIP 2 76 71.500000
#> 177 CTCF ChIP 2 77 11.166667
#> 178 CTCF ChIP 2 78 126.500000
#> 179 CTCF ChIP 2 79 NA
#> 180 CTCF ChIP 2 80 NA
#> 181 CTCF ChIP 2 81 5.500000
#> 182 CTCF ChIP 2 82 16.500000
#> 183 CTCF ChIP 2 83 NA
#> 184 CTCF ChIP 2 84 56.750000
#> 185 CTCF ChIP 2 85 NA
#> 186 CTCF ChIP 2 86 80.000000
#> 187 CTCF ChIP 2 87 126.500000
#> 188 CTCF ChIP 2 88 126.500000
#> 189 CTCF ChIP 2 89 99.500000
#> 190 CTCF ChIP 2 90 NA
#> 191 CTCF ChIP 2 91 71.500000
#> 192 CTCF ChIP 2 92 16.500000
#> 193 CTCF ChIP 2 93 69.000000
#> 194 CTCF ChIP 2 94 NA
#> 195 CTCF ChIP 2 95 16.500000
#> 196 CTCF ChIP 2 96 16.500000
#> 197 CTCF ChIP 2 97 71.500000
#> 198 CTCF ChIP 2 98 71.500000
#> 199 CTCF ChIP 2 99 126.500000
#> 200 CTCF ChIP 2 100 NA