This function will find the assays and features that match directly (by name) or indirectly (through aggregation) the feature name.
The subsetByFeature function will first identify the assay that
contains the feature(s) i and filter the rows matching these
feature names exactly. It will then find, in the other assays, the
features that produces i through aggregation with the
aggregateQFeatures function.
See QFeatures for an example.
An instance of class QFeatures.
A character of feature names present in an assay in x.
Additional parameters. Ignored.
An new instance of class QFeatures containing relevant assays and features.
example(aggregateFeatures)
#>
#> aggrgF> ## ---------------------------------------
#> aggrgF> ## An example QFeatures with PSM-level data
#> aggrgF> ## ---------------------------------------
#> aggrgF> data(feat1)
#>
#> aggrgF> feat1
#> An instance of class QFeatures containing 1 assays:
#> [1] psms: SummarizedExperiment with 10 rows and 2 columns
#>
#> aggrgF> ## Aggregate PSMs into peptides
#> aggrgF> feat1 <- aggregateFeatures(feat1, "psms", "Sequence", name = "peptides")
#>
#> aggrgF> feat1
#> An instance of class QFeatures containing 2 assays:
#> [1] psms: SummarizedExperiment with 10 rows and 2 columns
#> [2] peptides: SummarizedExperiment with 3 rows and 2 columns
#>
#> aggrgF> ## Aggregate peptides into proteins
#> aggrgF> feat1 <- aggregateFeatures(feat1, "peptides", "Protein", name = "proteins")
#>
#> aggrgF> feat1
#> An instance of class QFeatures containing 3 assays:
#> [1] psms: SummarizedExperiment with 10 rows and 2 columns
#> [2] peptides: SummarizedExperiment with 3 rows and 2 columns
#> [3] proteins: SummarizedExperiment with 2 rows and 2 columns
#>
#> aggrgF> assay(feat1[[1]])
#> S1 S2
#> PSM1 1 11
#> PSM2 2 12
#> PSM3 3 13
#> PSM4 4 14
#> PSM5 5 15
#> PSM6 6 16
#> PSM7 7 17
#> PSM8 8 18
#> PSM9 9 19
#> PSM10 10 20
#>
#> aggrgF> assay(feat1[[2]])
#> S1 S2
#> ELGNDAYK 5.0 15.0
#> IAEESNFPFIK 8.5 18.5
#> SYGFNAAR 2.0 12.0
#>
#> aggrgF> aggcounts(feat1[[2]])
#> S1 S2
#> ELGNDAYK 3 3
#> IAEESNFPFIK 4 4
#> SYGFNAAR 3 3
#>
#> aggrgF> assay(feat1[[3]])
#> S1 S2
#> ProtA 3.5 13.5
#> ProtB 8.5 18.5
#>
#> aggrgF> aggcounts(feat1[[3]])
#> S1 S2
#> ProtA 2 2
#> ProtB 1 1
#>
#> aggrgF> ## --------------------------------------------
#> aggrgF> ## Aggregation with missing quantitative values
#> aggrgF> ## --------------------------------------------
#> aggrgF> data(ft_na)
#>
#> aggrgF> ft_na
#> An instance of class QFeatures containing 1 assays:
#> [1] na: SummarizedExperiment with 4 rows and 3 columns
#>
#> aggrgF> assay(ft_na[[1]])
#> A B C
#> a NA 5 9
#> b 2 6 10
#> c 3 NA 11
#> d NA 8 12
#>
#> aggrgF> rowData(ft_na[[1]])
#> DataFrame with 4 rows and 2 columns
#> X Y
#> <integer> <character>
#> a 1 A
#> b 2 B
#> c 1 A
#> d 2 B
#>
#> aggrgF> ## By default, missing values are propagated
#> aggrgF> ft2 <- aggregateFeatures(ft_na, 1, fcol = "X", fun = colSums)
#> Your quantitative data contain missing values. Please read the relevant
#> section(s) in the aggregateFeatures manual page regarding the effects
#> of missing values on data aggregation.
#>
#> aggrgF> assay(ft2[[2]])
#> A B C
#> 1 NA NA 20
#> 2 NA 14 22
#>
#> aggrgF> aggcounts(ft2[[2]])
#> A B C
#> 1 1 1 2
#> 2 1 2 2
#>
#> aggrgF> ## The rowData .n variable tallies number of initial rows that
#> aggrgF> ## were aggregated (irrespective of NAs) for all the samples.
#> aggrgF> rowData(ft2[[2]])
#> DataFrame with 2 rows and 3 columns
#> X Y .n
#> <integer> <character> <integer>
#> 1 1 A 2
#> 2 2 B 2
#>
#> aggrgF> ## Ignored when setting na.rm = TRUE
#> aggrgF> ft3 <- aggregateFeatures(ft_na, 1, fcol = "X", fun = colSums, na.rm = TRUE)
#> Your quantitative data contain missing values. Please read the relevant
#> section(s) in the aggregateFeatures manual page regarding the effects
#> of missing values on data aggregation.
#>
#> aggrgF> assay(ft3[[2]])
#> A B C
#> 1 3 5 20
#> 2 2 14 22
#>
#> aggrgF> aggcounts(ft3[[2]])
#> A B C
#> 1 1 1 2
#> 2 1 2 2
#>
#> aggrgF> ## -----------------------------------------------
#> aggrgF> ## Aggregation with missing values in the row data
#> aggrgF> ## -----------------------------------------------
#> aggrgF> ## Row data results without any NAs, which includes the
#> aggrgF> ## Y variables
#> aggrgF> rowData(ft2[[2]])
#> DataFrame with 2 rows and 3 columns
#> X Y .n
#> <integer> <character> <integer>
#> 1 1 A 2
#> 2 2 B 2
#>
#> aggrgF> ## Missing value in the Y feature variable
#> aggrgF> rowData(ft_na[[1]])[1, "Y"] <- NA
#>
#> aggrgF> rowData(ft_na[[1]])
#> DataFrame with 4 rows and 2 columns
#> X Y
#> <integer> <character>
#> a 1 NA
#> b 2 B
#> c 1 A
#> d 2 B
#>
#> aggrgF> ft3 <- aggregateFeatures(ft_na, 1, fcol = "X", fun = colSums)
#> Your quantitative and row data contain missing values. Please read the
#> relevant section(s) in the aggregateFeatures manual page regarding the
#> effects of missing values on data aggregation.
#>
#> aggrgF> ## The Y feature variable has been dropped!
#> aggrgF> assay(ft3[[2]])
#> A B C
#> 1 NA NA 20
#> 2 NA 14 22
#>
#> aggrgF> rowData(ft3[[2]])
#> DataFrame with 2 rows and 2 columns
#> X .n
#> <integer> <integer>
#> 1 1 2
#> 2 2 2
#>
#> aggrgF> ## --------------------------------------------
#> aggrgF> ## Using a peptide-by-proteins adjacency matrix
#> aggrgF> ## --------------------------------------------
#> aggrgF>
#> aggrgF> ## Let's use assay peptides from object feat1 and
#> aggrgF> ## define that peptide SYGFNAAR maps to proteins
#> aggrgF> ## Prot A and B
#> aggrgF>
#> aggrgF> se <- feat1[["peptides"]]
#>
#> aggrgF> rowData(se)$Protein[3] <- c("ProtA;ProtB")
#>
#> aggrgF> rowData(se)
#> DataFrame with 3 rows and 4 columns
#> Sequence Protein location .n
#> <character> <character> <character> <integer>
#> ELGNDAYK ELGNDAYK ProtA Mitochondr... 3
#> IAEESNFPFIK IAEESNFPFI... ProtB unknown 4
#> SYGFNAAR SYGFNAAR ProtA;Prot... Mitochondr... 3
#>
#> aggrgF> ## This can also be defined using anadjacency matrix, manual
#> aggrgF> ## encoding here. See PSMatch::makeAdjacencyMatrix() for a
#> aggrgF> ## function that does it automatically.
#> aggrgF> adj <- matrix(0, nrow = 3, ncol = 2,
#> aggrgF+ dimnames = list(rownames(se),
#> aggrgF+ c("ProtA", "ProtB")))
#>
#> aggrgF> adj[1, 1] <- adj[2, 2] <- adj[3, 1:2] <- 1
#>
#> aggrgF> adj
#> ProtA ProtB
#> ELGNDAYK 1 0
#> IAEESNFPFIK 0 1
#> SYGFNAAR 1 1
#>
#> aggrgF> adjacencyMatrix(se) <- adj
#>
#> aggrgF> rowData(se)
#> DataFrame with 3 rows and 5 columns
#> Sequence Protein location .n adjacencyMatrix
#> <character> <character> <character> <integer> <dgCMatrix>
#> ELGNDAYK ELGNDAYK ProtA Mitochondr... 3 1:0
#> IAEESNFPFIK IAEESNFPFI... ProtB unknown 4 0:1
#> SYGFNAAR SYGFNAAR ProtA;Prot... Mitochondr... 3 1:1
#>
#> aggrgF> adjacencyMatrix(se)
#> 3 x 2 sparse Matrix of class "dgCMatrix"
#> ProtA ProtB
#> ELGNDAYK 1 .
#> IAEESNFPFIK . 1
#> SYGFNAAR 1 1
#>
#> aggrgF> ## Aggregation using the adjacency matrix
#> aggrgF> se2 <- aggregateFeatures(se, fcol = "adjacencyMatrix",
#> aggrgF+ fun = MsCoreUtils::colMeansMat)
#>
#> aggrgF> ## Peptide SYGFNAAR was taken into account in both ProtA and ProtB
#> aggrgF> ## aggregations.
#> aggrgF> assay(se2)
#> S1 S2
#> ProtA 3.50 13.50
#> ProtB 5.25 15.25
#>
#> aggrgF> ## Aggregation by matrix on a QFeature object works as with a
#> aggrgF> ## vector
#> aggrgF> ft <- QFeatures(list(peps = se))
#>
#> aggrgF> ft <- aggregateFeatures(ft, "peps", "adjacencyMatrix", name = "protsByMat",
#> aggrgF+ fun = MsCoreUtils::colMeansMat)
#>
#> aggrgF> assay(ft[[2]])
#> S1 S2
#> ProtA 3.50 13.50
#> ProtB 5.25 15.25
#>
#> aggrgF> rowData(ft[[2]])
#> DataFrame with 2 rows and 1 column
#> .n
#> <integer>
#> ProtA 2
#> ProtB 2
## Retrieve protein 'ProtA' and its 2 peptides and 6 PSMs
feat1["ProtA", , ]
#> An instance of class QFeatures containing 3 assays:
#> [1] psms: SummarizedExperiment with 6 rows and 2 columns
#> [2] peptides: SummarizedExperiment with 2 rows and 2 columns
#> [3] proteins: SummarizedExperiment with 1 rows and 2 columns