Converting a SummarizedExperiment object into a long data.frame

Source: R/meltAssay.R

meltSE Converts a SummarizedExperiment object into a long data.frame which can be used for tidyverse-tools.

meltSE(x, ...)

# S4 method for class 'SummarizedExperiment'
meltSE(
  x,
  assay.type = assay_name,
  assay_name = "counts",
  add.row = add_row_data,
  add_row_data = NULL,
  add.col = add_col_data,
  add_col_data = NULL,
  row.name = feature_name,
  feature_name = "FeatureID",
  col.name = sample_name,
  sample_name = "SampleID",
  ...
)

Arguments

x

TreeSummarizedExperiment.

...

optional arguments:

  • check.names: Logical scalar. Passed to data.frame function's check.name argument. Determines if sample names are checked that they are syntactically valid variable names and are not duplicated. If they are not, sample names are modified. (Default: TRUE)

assay.type

Character scalar. Specifies which assay to use for calculation. (Default: "counts")

assay_name

Deprecated. Use assay.type instead.

add.row

Logical scalar or Character vector. To select information from the rowData to add to the molten assay data. If add.row = NULL no data will be added, if add.row = TRUE all data will be added and if add.row is a character vector, it will be used to subset to given column names in rowData. (Default: NULL)

add_row_data

Deprecated. Use add.row instead.

add.col

Logical scalar. NULL, or character vector. Used to select information from the colData to add to the molten assay data. If add.col = NULL no data will be added, if add.col = TRUE all data will be added and if add.col is a character vector, it will be used to subset to given column names in colData. (Default: NULL)

add_col_data

Deprecated. Use add.col instead.

row.name

Character scalar. To use as the output's name for the feature identifier. (Default: "FeatureID")

feature_name

Deprecated. Use row.name instead.

col.name

Character scalar. To use as the output's name for the sample identifier. (Default: "SampleID")

sample_name

Deprecated. Use col.name instead.

Value

A tibble with the molten data. The assay values are given in a column named like the selected assay assay.type. In addition, a column “FeatureID” will contain the rownames, if set, and analogously a column “SampleID” with the colnames, if set.

Details

If the colData contains a column “SampleID” or the rowData contains a column “FeatureID”, they will be renamed to “SampleID_col” and “FeatureID_row”, if row names or column names are set.

Examples

data(GlobalPatterns)
molten_tse <- meltSE(
    GlobalPatterns,
    assay.type = "counts",
    add.row = TRUE,
    add.col = TRUE
    )
molten_tse
#> # A tibble: 499,616 × 17
#>    FeatureID SampleID counts Kingdom Phylum     Class Order Family Genus Species
#>    <fct>     <fct>     <dbl> <chr>   <chr>      <chr> <chr> <chr>  <chr> <chr>  
#>  1 549322    CL3           0 Archaea Crenarcha… Ther… NA    NA     NA    NA     
#>  2 549322    CC1           0 Archaea Crenarcha… Ther… NA    NA     NA    NA     
#>  3 549322    SV1           0 Archaea Crenarcha… Ther… NA    NA     NA    NA     
#>  4 549322    M31Fcsw       0 Archaea Crenarcha… Ther… NA    NA     NA    NA     
#>  5 549322    M11Fcsw       0 Archaea Crenarcha… Ther… NA    NA     NA    NA     
#>  6 549322    M31Plmr       0 Archaea Crenarcha… Ther… NA    NA     NA    NA     
#>  7 549322    M11Plmr       0 Archaea Crenarcha… Ther… NA    NA     NA    NA     
#>  8 549322    F21Plmr       0 Archaea Crenarcha… Ther… NA    NA     NA    NA     
#>  9 549322    M31Tong       0 Archaea Crenarcha… Ther… NA    NA     NA    NA     
#> 10 549322    M11Tong       0 Archaea Crenarcha… Ther… NA    NA     NA    NA     
#> # ℹ 499,606 more rows
#> # ℹ 7 more variables: X.SampleID <fct>, Primer <fct>, Final_Barcode <fct>,
#> #   Barcode_truncated_plus_T <fct>, Barcode_full_length <fct>,
#> #   SampleType <fct>, Description <fct>