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Subsetting AnyHermesData Objects

Source: R/HermesData-methods.R
subset.Rd

[Stable]

This method subsets AnyHermesData objects, based on expressions involving the rowData columns and the colData columns.

Arguments

x

(AnyHermesData)
object to subset from.

subset

(expression)
logical expression based on the rowData columns to select genes.

select

(expression)
logical expression based on the colData columns to select samples.

Value

The subsetted AnyHermesData object.

Note

Note that this just inherits SummarizedExperiment::subset,SummarizedExperiment-method().

Examples

a <- hermes_data
a
#> class: HermesData
#> assays(1): counts
#> genes(5085): GeneID:11185 GeneID:10677 ... GeneID:9087 GeneID:9426
#> additional gene information(3): GeneID SYMBOL chromosome_name
#> samples(20): 06520011B0023R 06520067C0018R ... 06520015C0016R
#>   06520019C0023R
#> additional sample information(72): Filename SampleID ... TTYPE STDSSDY

# Subset both genes and samples.
subset(a, subset = low_expression_flag, select = DISCSTUD == "N")
#> class: HermesData
#> assays(1): counts
#> genes(3021): GeneID:10677 GeneID:101928428 ... GeneID:9084 GeneID:9426
#> additional gene information(3): GeneID SYMBOL chromosome_name
#> samples(6): 06520067C0018R 06520105C0017R ... 06520023C0018R
#>   06520099B0017R
#> additional sample information(72): Filename SampleID ... TTYPE STDSSDY

# Subset only genes.
subset(a, subset = chromosome == "2")
#> class: HermesData
#> assays(1): counts
#> genes(326): GeneID:101929282 GeneID:51455 ... GeneID:101927614
#>   GeneID:285172
#> additional gene information(3): GeneID SYMBOL chromosome_name
#> samples(20): 06520011B0023R 06520067C0018R ... 06520015C0016R
#>   06520019C0023R
#> additional sample information(72): Filename SampleID ... TTYPE STDSSDY

# Subset only samples.
subset(a, select = AGE > 18)
#> class: HermesData
#> assays(1): counts
#> genes(5085): GeneID:11185 GeneID:10677 ... GeneID:9087 GeneID:9426
#> additional gene information(3): GeneID SYMBOL chromosome_name
#> samples(4): 06520011B0023R 06520103C0017R 06520001B0023R 06520080B0023R
#> additional sample information(72): Filename SampleID ... TTYPE STDSSDY