The longForm() method transform a QFeatures or SummarizedExperiment
instance into a long tidy DataFrame that contains the assay data, where
each quantitative value is reported on a separate line. colData and
rowData varibales can also be added. This function is an extension of the
longForm() method in the MultiAssayExperiment::MultiAssayExperiment.
Note that the previous longFormat implementation is not defunct.
Usage
# S4 method for class 'QFeatures'
longForm(object, colvars = NULL, rowvars = NULL, i = 1L)
# S4 method for class 'SummarizedExperiment'
longForm(object, colvars = NULL, rowvars = NULL, i = seq_along(assays(object)))Arguments
- object
An instance of class QFeatures or SummarizedExperiment.
- colvars
A
character()that selects column(s) in thecolData.- rowvars
A
character()with the names of therowDatavariables (columns) to retain in any assay.- i
When
objectis an instance of classQFeatures, anumeric(1)indicating what assay within eachSummarizedExperimentobject to return. Default is1L. Ifobjectis aSummarizedExperiment, anumeric()indicating what assays to pull and convert. Default is to use all assays.
Examples
data(feat2)
longForm(feat2)
#> DataFrame with 84 rows and 5 columns
#> assay primary rowname colname value
#> <character> <character> <character> <character> <numeric>
#> 1 assay1 S1 a S1 1
#> 2 assay1 S1 b S1 2
#> 3 assay1 S1 c S1 3
#> 4 assay1 S1 d S1 4
#> 5 assay1 S1 e S1 5
#> ... ... ... ... ... ...
#> 80 assay3 S12 j S12 24
#> 81 assay3 S12 k S12 25
#> 82 assay3 S12 l S12 26
#> 83 assay3 S12 m S12 27
#> 84 assay3 S12 n S12 28
## add a colData variable and use it in longFrom
colData(feat2)$colvar <- paste0("Var", 1:12)
colData(feat2)
#> DataFrame with 12 rows and 1 column
#> colvar
#> <character>
#> S1 Var1
#> S2 Var2
#> S3 Var3
#> S4 Var4
#> S5 Var5
#> ... ...
#> S8 Var8
#> S9 Var9
#> S10 Var10
#> S11 Var11
#> S12 Var12
longForm(feat2, colvars = "colvar")
#> DataFrame with 84 rows and 6 columns
#> assay primary rowname colname value colvar
#> <character> <character> <character> <character> <numeric> <character>
#> 1 assay1 S1 a S1 1 Var1
#> 2 assay1 S1 b S1 2 Var1
#> 3 assay1 S1 c S1 3 Var1
#> 4 assay1 S1 d S1 4 Var1
#> 5 assay1 S1 e S1 5 Var1
#> ... ... ... ... ... ... ...
#> 80 assay3 S12 j S12 24 Var12
#> 81 assay3 S12 k S12 25 Var12
#> 82 assay3 S12 l S12 26 Var12
#> 83 assay3 S12 m S12 27 Var12
#> 84 assay3 S12 n S12 28 Var12
## use a rowData variable in longFrom
rowDataNames(feat2)
#> CharacterList of length 3
#> [["assay1"]] Prot x
#> [["assay2"]] Prot x y
#> [["assay3"]] Prot x y
longForm(feat2, rowvar = "Prot")
#> DataFrame with 84 rows and 6 columns
#> assay primary rowname colname value Prot
#> <character> <character> <character> <character> <numeric> <character>
#> 1 assay1 S1 a S1 1 Pa
#> 2 assay1 S1 b S1 2 Pb
#> 3 assay1 S1 c S1 3 Pc
#> 4 assay1 S1 d S1 4 Pd
#> 5 assay1 S1 e S1 5 Pe
#> ... ... ... ... ... ... ...
#> 80 assay3 S12 j S12 24 Pj
#> 81 assay3 S12 k S12 25 Pk
#> 82 assay3 S12 l S12 26 Pl
#> 83 assay3 S12 m S12 27 Pm
#> 84 assay3 S12 n S12 28 Pn
## use both col/rowData
longForm(feat2, colvar = "colvar", rowvar = "Prot")
#> DataFrame with 84 rows and 7 columns
#> assay primary rowname colname value colvar
#> <character> <character> <character> <character> <numeric> <character>
#> 1 assay1 S1 a S1 1 Var1
#> 2 assay1 S1 b S1 2 Var1
#> 3 assay1 S1 c S1 3 Var1
#> 4 assay1 S1 d S1 4 Var1
#> 5 assay1 S1 e S1 5 Var1
#> ... ... ... ... ... ... ...
#> 80 assay3 S12 j S12 24 Var12
#> 81 assay3 S12 k S12 25 Var12
#> 82 assay3 S12 l S12 26 Var12
#> 83 assay3 S12 m S12 27 Var12
#> 84 assay3 S12 n S12 28 Var12
#> Prot
#> <character>
#> 1 Pa
#> 2 Pb
#> 3 Pc
#> 4 Pd
#> 5 Pe
#> ... ...
#> 80 Pj
#> 81 Pk
#> 82 Pl
#> 83 Pm
#> 84 Pn
## also works on a single SE
se <- getWithColData(feat2, 1)
#> Warning: 'experiments' dropped; see 'drops()'
longForm(se)
#> DataFrame with 40 rows and 4 columns
#> rowname colname value assayName
#> <character> <character> <numeric> <integer>
#> 1 a S1 1 1
#> 2 b S1 2 1
#> 3 c S1 3 1
#> 4 d S1 4 1
#> 5 e S1 5 1
#> ... ... ... ... ...
#> 36 f S4 36 1
#> 37 g S4 37 1
#> 38 h S4 38 1
#> 39 i S4 39 1
#> 40 j S4 40 1
longForm(se, colvar = "colvar")
#> DataFrame with 40 rows and 5 columns
#> rowname colname value assayName colvar
#> <character> <character> <numeric> <integer> <character>
#> 1 a S1 1 1 Var1
#> 2 b S1 2 1 Var1
#> 3 c S1 3 1 Var1
#> 4 d S1 4 1 Var1
#> 5 e S1 5 1 Var1
#> ... ... ... ... ... ...
#> 36 f S4 36 1 Var4
#> 37 g S4 37 1 Var4
#> 38 h S4 38 1 Var4
#> 39 i S4 39 1 Var4
#> 40 j S4 40 1 Var4
longForm(se, rowvar = "Prot")
#> DataFrame with 40 rows and 5 columns
#> rowname colname value assayName Prot
#> <character> <character> <numeric> <integer> <character>
#> 1 a S1 1 1 Pa
#> 2 b S1 2 1 Pb
#> 3 c S1 3 1 Pc
#> 4 d S1 4 1 Pd
#> 5 e S1 5 1 Pe
#> ... ... ... ... ... ...
#> 36 f S4 36 1 Pf
#> 37 g S4 37 1 Pg
#> 38 h S4 38 1 Ph
#> 39 i S4 39 1 Pi
#> 40 j S4 40 1 Pj
longForm(se, colvar = "colvar", rowvar = "Prot")
#> DataFrame with 40 rows and 6 columns
#> rowname colname value assayName colvar Prot
#> <character> <character> <numeric> <integer> <character> <character>
#> 1 a S1 1 1 Var1 Pa
#> 2 b S1 2 1 Var1 Pb
#> 3 c S1 3 1 Var1 Pc
#> 4 d S1 4 1 Var1 Pd
#> 5 e S1 5 1 Var1 Pe
#> ... ... ... ... ... ... ...
#> 36 f S4 36 1 Var4 Pf
#> 37 g S4 37 1 Var4 Pg
#> 38 h S4 38 1 Var4 Ph
#> 39 i S4 39 1 Var4 Pi
#> 40 j S4 40 1 Var4 Pj