Extract one or more (possibly nested) columns from the colData of a SummarizedExperiment object

Usage

extractColDataColumns(
  se,
  colNames,
  alignWith = ifelse(any(grepl(":", colNames)), "read", "sample")
)

Arguments

se: A SummarizedExperiment object.
colNames: A character vector corresponding to the names of annotation (colData) columns to extract and consolidate into a data.frame. The names can be either columns of colData(se) itself, or columns in a nested (read-level) annotation column of colData(se). In the latter case, the colNames should be of the form outerColName:innerColName, where outerColName is a column name in colData(se), and innerColName is a column name in each element of colData(se)[[outerColName]].
alignWith: A character scalar indicating whether the rows in the returned data.frame correspond to reads ("read") or samples ("sample"). If any element of colNames refers to a nested column, alignWith must be "read".

Value

A data.frame with columns sample, read (if alignWith = "read") and make.names(colNames).

Author

Michael Stadler, Charlotte Soneson

Examples

extractfiles <- system.file("extdata",
                            c("modkit_extract_rc_6mA_1.tsv.gz",
                              "modkit_extract_rc_6mA_2.tsv.gz"),
                            package = "SingleMoleculeGenomicsIO")
se <- readModkitExtract(extractfiles, modbase = "a", filter = "modkit",
                        BPPARAM = BiocParallel::SerialParam())
df <- extractColDataColumns(se = se,
                            colNames = c("modbase", "readInfo:ref_strand"),
                            alignWith = "read")
head(df)
#>     sample                                    read readInfo.ref_strand modbase
#> s11     s1 s1-233e48a7-f379-4dcf-9270-958231125563                   -       a
#> s12     s1 s1-d52a5f6a-a60a-4f85-913e-eada84bfbfb9                   -       a
#> s13     s1 s1-fc4646ce-66f9-401f-b968-e9b0cda14d61                   +       a
#> s14     s1 s1-92e906ae-cddb-4347-a114-bf9137761a8d                   -       a
#> s15     s1 s1-6cf74134-e550-4c02-bd2b-91385422ee25                   +       a
#> s16     s1 s1-5d45d8d2-d5f5-47ff-a9fa-f3fd6b7bd3c7                   +       a
dim(df)
#> [1] 20  4
df <- extractColDataColumns(se = se,
                            colNames = "modbase",
                            alignWith = "sample")
head(df)
#>   sample modbase
#> 1     s1       a
#> 2     s2       a
dim(df)
#> [1] 2 2