Mutate the sample or variable information of an experiment() or
SummarizedExperiment.
The same syntax as dplyr::mutate() is used.
For example, to add a new column to the sample information tibble,
use mutate_col(exp, new_column = value).
This actually calls dplyr::mutate() on the sample information tibble
with new_column = value.
If an identifier column is modified, its new values must be unique; otherwise, an error is thrown. The assay column names or row names will be updated accordingly.
Arguments
- exp
An
experiment()orSummarizedExperimentobject.- ...
<
data-masking> Name-value pairs, passed todplyr::mutate()internally.
Identifier columns
For an experiment() object, sample is a physical column in
sample_info, and variable is a physical column in var_info.
For a SummarizedExperiment, sample and variable identifiers live in
colnames(exp) and rownames(exp), rather than in
SummarizedExperiment::colData() or SummarizedExperiment::rowData().
Observation verbs expose colnames(exp) as a virtual .sample column, and
variable verbs expose rownames(exp) as a virtual .variable column. These
dot-prefixed names distinguish dimension identifiers from regular metadata
columns. After the operation, the virtual column is removed and its values
are written back to the corresponding dimension names.
Consequently, sample in colData(exp) and variable in rowData(exp)
remain ordinary metadata columns. The names .sample and .variable are
reserved; an input containing either name in the corresponding metadata
raises an error rather than overwriting that column.
Examples
library(SummarizedExperiment)
# Add metadata to a bundled experiment
exp <- real_experiment |>
mutate_row(type = "glycopeptide")
# Add a new column to sample information tibble or variable information tibble
exp |>
mutate_col(new_column = 1) |>
colData()
#> DataFrame with 12 rows and 2 columns
#> group new_column
#> <factor> <numeric>
#> C1 C 1
#> C2 C 1
#> C3 C 1
#> H1 H 1
#> H2 H 1
#> ... ... ...
#> M2 M 1
#> M3 M 1
#> Y1 Y 1
#> Y2 Y 1
#> Y3 Y 1
exp |>
mutate_row(new_column = "A") |>
rowData()
#> DataFrame with 4262 rows and 9 columns
#> peptide
#> <character>
#> P08185-176-Hex(5)HexNAc(4)NeuAc(2) NKTQGK
#> P04196-344-Hex(5)HexNAc(4)NeuAc(1)-1 HSHNNNSSDLHPHK
#> P04196-344-Hex(5)HexNAc(4) HSHNNNSSDLHPHK
#> P04196-344-Hex(5)HexNAc(4)NeuAc(1)-2 HSHNNNSSDLHPHK
#> P10909-291-Hex(6)HexNAc(5)-1 HNSTGCLR
#> ... ...
#> P09871-174-Hex(5)HexNAc(4)NeuAc(1) NCGVNCSGDVFTALIGEIAS..
#> P02763-93-Hex(7)HexNAc(6)dHex(1)NeuAc(4)-2 QDQCIYNTTYLNVQR
#> P02790-453-Hex(6)HexNAc(5)NeuAc(3)-2 ALPQPQNVTSLLGCTH
#> P01008-187-Hex(12)HexNAc(2) SLTFNETYQDISELVYGAK
#> P01023-1424-Hex(5)HexNAc(4)dHex(1)NeuAc(1)-2 VSNQTLSLFFTVLQDVPVR
#> peptide_site protein
#> <integer> <character>
#> P08185-176-Hex(5)HexNAc(4)NeuAc(2) 1 P08185
#> P04196-344-Hex(5)HexNAc(4)NeuAc(1)-1 5 P04196
#> P04196-344-Hex(5)HexNAc(4) 5 P04196
#> P04196-344-Hex(5)HexNAc(4)NeuAc(1)-2 5 P04196
#> P10909-291-Hex(6)HexNAc(5)-1 2 P10909
#> ... ... ...
#> P09871-174-Hex(5)HexNAc(4)NeuAc(1) 5 P09871
#> P02763-93-Hex(7)HexNAc(6)dHex(1)NeuAc(4)-2 7 P02763
#> P02790-453-Hex(6)HexNAc(5)NeuAc(3)-2 7 P02790
#> P01008-187-Hex(12)HexNAc(2) 5 P01008
#> P01023-1424-Hex(5)HexNAc(4)dHex(1)NeuAc(1)-2 3 P01023
#> protein_site gene
#> <integer> <character>
#> P08185-176-Hex(5)HexNAc(4)NeuAc(2) 176 SERPINA6
#> P04196-344-Hex(5)HexNAc(4)NeuAc(1)-1 344 HRG
#> P04196-344-Hex(5)HexNAc(4) 344 HRG
#> P04196-344-Hex(5)HexNAc(4)NeuAc(1)-2 344 HRG
#> P10909-291-Hex(6)HexNAc(5)-1 291 CLU
#> ... ... ...
#> P09871-174-Hex(5)HexNAc(4)NeuAc(1) 174 C1S
#> P02763-93-Hex(7)HexNAc(6)dHex(1)NeuAc(4)-2 93 ORM1
#> P02790-453-Hex(6)HexNAc(5)NeuAc(3)-2 453 HPX
#> P01008-187-Hex(12)HexNAc(2) 187 SERPINC1
#> P01023-1424-Hex(5)HexNAc(4)dHex(1)NeuAc(1)-2 1424 A2M
#> glycan_composition
#> <glyrepr_composition>
#> P08185-176-Hex(5)HexNAc(4)NeuAc(2) Hex(5)HexNAc(4)NeuAc..
#> P04196-344-Hex(5)HexNAc(4)NeuAc(1)-1 Hex(5)HexNAc(4)NeuAc..
#> P04196-344-Hex(5)HexNAc(4) Hex(5)HexNAc(4)
#> P04196-344-Hex(5)HexNAc(4)NeuAc(1)-2 Hex(5)HexNAc(4)NeuAc..
#> P10909-291-Hex(6)HexNAc(5)-1 Hex(6)HexNAc(5)
#> ... ...
#> P09871-174-Hex(5)HexNAc(4)NeuAc(1) Hex(5)HexNAc(4)NeuAc..
#> P02763-93-Hex(7)HexNAc(6)dHex(1)NeuAc(4)-2 Hex(7)HexNAc(6)dHex(..
#> P02790-453-Hex(6)HexNAc(5)NeuAc(3)-2 Hex(6)HexNAc(5)NeuAc..
#> P01008-187-Hex(12)HexNAc(2) Hex(12)HexNAc(2)
#> P01023-1424-Hex(5)HexNAc(4)dHex(1)NeuAc(1)-2 Hex(5)HexNAc(4)dHex(..
#> glycan_structure
#> <glyrepr_structure>
#> P08185-176-Hex(5)HexNAc(4)NeuAc(2) NeuAc(??-?)Hex(??-?)..
#> P04196-344-Hex(5)HexNAc(4)NeuAc(1)-1 NeuAc(??-?)Hex(??-?)..
#> P04196-344-Hex(5)HexNAc(4) Hex(??-?)HexNAc(??-?..
#> P04196-344-Hex(5)HexNAc(4)NeuAc(1)-2 NeuAc(??-?)Hex(??-?)..
#> P10909-291-Hex(6)HexNAc(5)-1 Hex(??-?)HexNAc(??-?..
#> ... ...
#> P09871-174-Hex(5)HexNAc(4)NeuAc(1) NeuAc(??-?)Hex(??-?)..
#> P02763-93-Hex(7)HexNAc(6)dHex(1)NeuAc(4)-2 NeuAc(??-?)Hex(??-?)..
#> P02790-453-Hex(6)HexNAc(5)NeuAc(3)-2 NeuAc(??-?)Hex(??-?)..
#> P01008-187-Hex(12)HexNAc(2) Hex(??-?)Hex(??-?)He..
#> P01023-1424-Hex(5)HexNAc(4)dHex(1)NeuAc(1)-2 NeuAc(??-?)Hex(??-?)..
#> type new_column
#> <character> <character>
#> P08185-176-Hex(5)HexNAc(4)NeuAc(2) glycopeptide A
#> P04196-344-Hex(5)HexNAc(4)NeuAc(1)-1 glycopeptide A
#> P04196-344-Hex(5)HexNAc(4) glycopeptide A
#> P04196-344-Hex(5)HexNAc(4)NeuAc(1)-2 glycopeptide A
#> P10909-291-Hex(6)HexNAc(5)-1 glycopeptide A
#> ... ... ...
#> P09871-174-Hex(5)HexNAc(4)NeuAc(1) glycopeptide A
#> P02763-93-Hex(7)HexNAc(6)dHex(1)NeuAc(4)-2 glycopeptide A
#> P02790-453-Hex(6)HexNAc(5)NeuAc(3)-2 glycopeptide A
#> P01008-187-Hex(12)HexNAc(2) glycopeptide A
#> P01023-1424-Hex(5)HexNAc(4)dHex(1)NeuAc(1)-2 glycopeptide A
# Modify existing columns
exp |>
mutate_col(group = dplyr::if_else(group == "H", "healthy", "other")) |>
colData()
#> DataFrame with 12 rows and 1 column
#> group
#> <character>
#> C1 other
#> C2 other
#> C3 other
#> H1 healthy
#> H2 healthy
#> ... ...
#> M2 other
#> M3 other
#> Y1 other
#> Y2 other
#> Y3 other
exp |>
mutate_row(type = dplyr::if_else(type == "glycopeptide", "good", "bad")) |>
rowData()
#> DataFrame with 4262 rows and 8 columns
#> peptide
#> <character>
#> P08185-176-Hex(5)HexNAc(4)NeuAc(2) NKTQGK
#> P04196-344-Hex(5)HexNAc(4)NeuAc(1)-1 HSHNNNSSDLHPHK
#> P04196-344-Hex(5)HexNAc(4) HSHNNNSSDLHPHK
#> P04196-344-Hex(5)HexNAc(4)NeuAc(1)-2 HSHNNNSSDLHPHK
#> P10909-291-Hex(6)HexNAc(5)-1 HNSTGCLR
#> ... ...
#> P09871-174-Hex(5)HexNAc(4)NeuAc(1) NCGVNCSGDVFTALIGEIAS..
#> P02763-93-Hex(7)HexNAc(6)dHex(1)NeuAc(4)-2 QDQCIYNTTYLNVQR
#> P02790-453-Hex(6)HexNAc(5)NeuAc(3)-2 ALPQPQNVTSLLGCTH
#> P01008-187-Hex(12)HexNAc(2) SLTFNETYQDISELVYGAK
#> P01023-1424-Hex(5)HexNAc(4)dHex(1)NeuAc(1)-2 VSNQTLSLFFTVLQDVPVR
#> peptide_site protein
#> <integer> <character>
#> P08185-176-Hex(5)HexNAc(4)NeuAc(2) 1 P08185
#> P04196-344-Hex(5)HexNAc(4)NeuAc(1)-1 5 P04196
#> P04196-344-Hex(5)HexNAc(4) 5 P04196
#> P04196-344-Hex(5)HexNAc(4)NeuAc(1)-2 5 P04196
#> P10909-291-Hex(6)HexNAc(5)-1 2 P10909
#> ... ... ...
#> P09871-174-Hex(5)HexNAc(4)NeuAc(1) 5 P09871
#> P02763-93-Hex(7)HexNAc(6)dHex(1)NeuAc(4)-2 7 P02763
#> P02790-453-Hex(6)HexNAc(5)NeuAc(3)-2 7 P02790
#> P01008-187-Hex(12)HexNAc(2) 5 P01008
#> P01023-1424-Hex(5)HexNAc(4)dHex(1)NeuAc(1)-2 3 P01023
#> protein_site gene
#> <integer> <character>
#> P08185-176-Hex(5)HexNAc(4)NeuAc(2) 176 SERPINA6
#> P04196-344-Hex(5)HexNAc(4)NeuAc(1)-1 344 HRG
#> P04196-344-Hex(5)HexNAc(4) 344 HRG
#> P04196-344-Hex(5)HexNAc(4)NeuAc(1)-2 344 HRG
#> P10909-291-Hex(6)HexNAc(5)-1 291 CLU
#> ... ... ...
#> P09871-174-Hex(5)HexNAc(4)NeuAc(1) 174 C1S
#> P02763-93-Hex(7)HexNAc(6)dHex(1)NeuAc(4)-2 93 ORM1
#> P02790-453-Hex(6)HexNAc(5)NeuAc(3)-2 453 HPX
#> P01008-187-Hex(12)HexNAc(2) 187 SERPINC1
#> P01023-1424-Hex(5)HexNAc(4)dHex(1)NeuAc(1)-2 1424 A2M
#> glycan_composition
#> <glyrepr_composition>
#> P08185-176-Hex(5)HexNAc(4)NeuAc(2) Hex(5)HexNAc(4)NeuAc..
#> P04196-344-Hex(5)HexNAc(4)NeuAc(1)-1 Hex(5)HexNAc(4)NeuAc..
#> P04196-344-Hex(5)HexNAc(4) Hex(5)HexNAc(4)
#> P04196-344-Hex(5)HexNAc(4)NeuAc(1)-2 Hex(5)HexNAc(4)NeuAc..
#> P10909-291-Hex(6)HexNAc(5)-1 Hex(6)HexNAc(5)
#> ... ...
#> P09871-174-Hex(5)HexNAc(4)NeuAc(1) Hex(5)HexNAc(4)NeuAc..
#> P02763-93-Hex(7)HexNAc(6)dHex(1)NeuAc(4)-2 Hex(7)HexNAc(6)dHex(..
#> P02790-453-Hex(6)HexNAc(5)NeuAc(3)-2 Hex(6)HexNAc(5)NeuAc..
#> P01008-187-Hex(12)HexNAc(2) Hex(12)HexNAc(2)
#> P01023-1424-Hex(5)HexNAc(4)dHex(1)NeuAc(1)-2 Hex(5)HexNAc(4)dHex(..
#> glycan_structure type
#> <glyrepr_structure> <character>
#> P08185-176-Hex(5)HexNAc(4)NeuAc(2) NeuAc(??-?)Hex(??-?).. good
#> P04196-344-Hex(5)HexNAc(4)NeuAc(1)-1 NeuAc(??-?)Hex(??-?).. good
#> P04196-344-Hex(5)HexNAc(4) Hex(??-?)HexNAc(??-?.. good
#> P04196-344-Hex(5)HexNAc(4)NeuAc(1)-2 NeuAc(??-?)Hex(??-?).. good
#> P10909-291-Hex(6)HexNAc(5)-1 Hex(??-?)HexNAc(??-?.. good
#> ... ... ...
#> P09871-174-Hex(5)HexNAc(4)NeuAc(1) NeuAc(??-?)Hex(??-?).. good
#> P02763-93-Hex(7)HexNAc(6)dHex(1)NeuAc(4)-2 NeuAc(??-?)Hex(??-?).. good
#> P02790-453-Hex(6)HexNAc(5)NeuAc(3)-2 NeuAc(??-?)Hex(??-?).. good
#> P01008-187-Hex(12)HexNAc(2) Hex(??-?)Hex(??-?)He.. good
#> P01023-1424-Hex(5)HexNAc(4)dHex(1)NeuAc(1)-2 NeuAc(??-?)Hex(??-?).. good
# SummarizedExperiment identifiers use virtual dot-prefixed columns
mutate_col(exp, .sample = paste0("new_", .sample))
#>
#> ── GlycoproteomicSE ────────────────────────────────────────────────────────────
#> ℹ Abundance assay: 12 samples, 4262 variables
#> ℹ Glycan type: N
#> ℹ Row data fields: peptide <chr>, peptide_site <int>, protein <chr>, protein_site <int>, gene <chr>, glycan_composition <comp>, glycan_structure <struct>, type <chr>
#> ℹ Column data fields: group <fct>
#> ℹ Metadata fields: exp_type <chr>, glycan_type <chr>, quant_method <chr>
mutate_row(exp, .variable = paste0("new_", .variable))
#>
#> ── GlycoproteomicSE ────────────────────────────────────────────────────────────
#> ℹ Abundance assay: 12 samples, 4262 variables
#> ℹ Glycan type: N
#> ℹ Row data fields: peptide <chr>, peptide_site <int>, protein <chr>, protein_site <int>, gene <chr>, glycan_composition <comp>, glycan_structure <struct>, type <chr>
#> ℹ Column data fields: group <fct>
#> ℹ Metadata fields: exp_type <chr>, glycan_type <chr>, quant_method <chr>