Skip to contents

Retrieve log R ratio from Bulk data on single-cell features (internal)

Source: R/computeLogRatio.R
getLogRatioBulk.Rd

This internal function assigns the log R ratio (LRR) values from bulk data segments to single-cell omic features. It matches the bulk data segments to corresponding genomic features from the single-cell omic data and returns a table of single-cell features with the corresponding bulk LRR values.

Usage

getLogRatioBulk(x, bulk.lrr)

Arguments

x

A muscomic object containing the single-cell omic data, which includes the feature coordinates (muscomic).

bulk.lrr

A data frame containing log R ratio per genomic segments from bulk sequencing data (data.frame). One row per segment and 4 columns ordered as followed: chromosome (integer), start position (integer), end position (integer), and Log R ratio value (numeric).

Value

A data frame of single-cell omic features, with columns: CHROM, start, end, and bulk.lrr, where bulk.lrr corresponds to the log R ratio values retrieved from bulk data matching the feature coordinates.

See also

example data: bulk_lrr functions: muscomic, muscadet

Examples

# Create a muscomic object
atac <- CreateMuscomicObject(
  type = "ATAC",
  mat_counts = mat_counts_atac_tumor,
  allele_counts = allele_counts_atac_tumor,
  features = peaks
)
# or use a muscomic object inside a muscadet object
atac <- slot(muscadet_obj, "omics")[["ATAC"]]

# Load bulk Log R ratio data frame
data(bulk_lrr)
head(bulk_lrr)
#>   CHROM     start       end         lrr
#> 1     1     16100  78558400 -0.17422897
#> 2     1  78558700  80533900 -0.85006857
#> 3     1  80534279  80603200 -0.17219191
#> 4     1  80603500  99964900 -0.86685361
#> 5     1  99965200 122514900 -0.15990417
#> 6     1 122520400 124588600  0.05119736
# or use the one inside a muscadet object
head(slot(muscadet_obj, "bulk.data")[["log.ratio"]])
#>   CHROM     start       end         lrr
#> 1     1     16100  78558400 -0.17422897
#> 2     1  78558700  80533900 -0.85006857
#> 3     1  80534279  80603200 -0.17219191
#> 4     1  80603500  99964900 -0.86685361
#> 5     1  99965200 122514900 -0.15990417
#> 6     1 122520400 124588600  0.05119736

features_bulk_lrr <- getLogRatioBulk(
  x = atac,
  bulk.lrr = bulk_lrr # or slot(muscadet_obj, "bulk.data")[["log.ratio"]]
)
head(features_bulk_lrr)
#>   CHROM     start       end   bulk.lrr
#> 1     1 102000001 112000000 -0.1599042
#> 2     1 104000001 114000000 -0.1599042
#> 3     1 106000001 116000000 -0.1599042
#> 4     1 108000001 118000000 -0.1599042
#> 5     1 110000001 120000000 -0.1599042
#> 6     1 228000001 238000000 -0.1641702