Write bigWig tracks per sample or group

Export bigWig files with per-window scores for each sample (or group means).

writeBigWigs(
  qseaSet,
  folderName,
  normMethod = "nrpm",
  useGroupMeans = FALSE,
  naVal = -1
)

Arguments

qseaSet

qseaSet. A qseaSet object containing methylation-enriched sequencing data. Default: none (must be supplied).

folderName

character(1). Output directory where .bw files will be written (created if missing). Default: none (must be supplied).

normMethod

character(1). Normalisation/measure to export. Common choices: "nrpm" or "beta". Default: "nrpm".

useGroupMeans

logical(1). If TRUE, export group-mean tracks instead of per-sample tracks. Default: FALSE.

naVal

numeric(1). Value used to replace NA scores prior to export (useful for beta). Default: 0.

Value

(Invisibly) NULL. Files are written to folderName.

Details

For each sample (or group), the function pairs the per-window scores from qseaSet with the corresponding window genomic coordinates and writes a bigWig via rtracklayer. When exporting beta, windows failing the minimum read threshold used to compute beta may be NA; these are replaced by naVal before writing.

File naming. Output files are typically named using the sample (or group) name and the method, e.g. "<sample>_<method>.bw" or "<group>_<method>_means.bw" when useGroupMeans = TRUE.

Seqinfo. bigWig export requires chromosome lengths; ensure the window GRanges in qseaSet carries valid seqinfo (this is the case for the example data on GRCh38).

See also

getDataTable()

Examples

data(exampleTumourNormal, package = "mesa")

# Per-sample NRPM bigWigs
td <- tempfile()
dir.create(td)
exampleTumourNormal %>%
  writeBigWigs(folderName = td, normMethod = "nrpm", useGroupMeans = FALSE)
#> Generating table of nrpm values for 819 regions across 10 samples.
#> Writing bigWig track to /tmp/RtmpP8NbUt/file51732344a45/Colon1_N_nrpm.bw
#> Writing bigWig track to /tmp/RtmpP8NbUt/file51732344a45/Colon1_T_nrpm.bw
#> Writing bigWig track to /tmp/RtmpP8NbUt/file51732344a45/Colon2_N_nrpm.bw
#> Writing bigWig track to /tmp/RtmpP8NbUt/file51732344a45/Colon2_T_nrpm.bw
#> Writing bigWig track to /tmp/RtmpP8NbUt/file51732344a45/Lung1_N_nrpm.bw
#> Writing bigWig track to /tmp/RtmpP8NbUt/file51732344a45/Lung1_T_nrpm.bw
#> Writing bigWig track to /tmp/RtmpP8NbUt/file51732344a45/Lung2_N_nrpm.bw
#> Writing bigWig track to /tmp/RtmpP8NbUt/file51732344a45/Lung2_T_nrpm.bw
#> Writing bigWig track to /tmp/RtmpP8NbUt/file51732344a45/Lung3_N_nrpm.bw
#> Writing bigWig track to /tmp/RtmpP8NbUt/file51732344a45/Lung3_T_nrpm.bw
list.files(td, pattern = "\\\\.bw$")
#> character(0)

# Group-mean beta bigWigs (replace NA beta with 0)
td2 <- tempfile()
dir.create(td2)
exampleTumourNormal %>%
  writeBigWigs(
      folderName = td2,
      normMethod = "beta",
      useGroupMeans = TRUE,
      naVal = 0
  )
#> Generating table of beta values for 819 regions across 10 sample groups.
#> Writing bigWig track to /tmp/RtmpP8NbUt/file517788f8746/Colon1_N_beta.bw
#> Writing bigWig track to /tmp/RtmpP8NbUt/file517788f8746/Colon1_T_beta.bw
#> Writing bigWig track to /tmp/RtmpP8NbUt/file517788f8746/Colon2_N_beta.bw
#> Writing bigWig track to /tmp/RtmpP8NbUt/file517788f8746/Colon2_T_beta.bw
#> Writing bigWig track to /tmp/RtmpP8NbUt/file517788f8746/Lung1_N_beta.bw
#> Writing bigWig track to /tmp/RtmpP8NbUt/file517788f8746/Lung1_T_beta.bw
#> Writing bigWig track to /tmp/RtmpP8NbUt/file517788f8746/Lung2_N_beta.bw
#> Writing bigWig track to /tmp/RtmpP8NbUt/file517788f8746/Lung2_T_beta.bw
#> Writing bigWig track to /tmp/RtmpP8NbUt/file517788f8746/Lung3_N_beta.bw
#> Writing bigWig track to /tmp/RtmpP8NbUt/file517788f8746/Lung3_T_beta.bw
list.files(td, pattern = "\\\\.bw$")
#> character(0)