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join_features

Source: R/methods.R
join_features.Rd

join_features() extracts and joins information for specific features

Usage

# S4 method for class 'Seurat'
join_features(
  .data,
  features = NULL,
  all = FALSE,
  exclude_zeros = FALSE,
  shape = "long",
  assay = NULL,
  slot = "data",
  ...
)

Arguments

.data

A tidyseurat object

features

A vector of feature identifiers to join

all

If TRUE return all

exclude_zeros

If TRUE exclude zero values

shape

Format of the returned table "long" or "wide"

assay

assay name to extract feature abundance

slot

slot name to extract feature abundance

...

Parameters to pass to join wide, i.e. assay name to extract feature abundance from and gene prefix, for shape="wide"

Value

A `tidyseurat` object containing information for the specified features.

Details

This function extracts information for specified features and returns the information in either long or wide format.

Examples

data(pbmc_small)
pbmc_small %>% join_features(
  features=c("HLA-DRA", "LYZ"))
#> tidyseurat says: This operation lead to duplicated cell names. A data frame is returned for independent data analysis.
#> # A tibble: 160 × 31
#>    .cell          .feature .abundance_RNA orig.ident    nCount_RNA nFeature_RNA
#>    <chr>          <chr>             <dbl> <fct>              <dbl>        <int>
#>  1 ATGCCAGAACGACT HLA-DRA            0    SeuratProject         70           47
#>  2 ATGCCAGAACGACT LYZ                4.97 SeuratProject         70           47
#>  3 CATGGCCTGTGCAT HLA-DRA            4.78 SeuratProject         85           52
#>  4 CATGGCCTGTGCAT LYZ                4.78 SeuratProject         85           52
#>  5 GAACCTGATGAACC HLA-DRA            0    SeuratProject         87           50
#>  6 GAACCTGATGAACC LYZ                4.75 SeuratProject         87           50
#>  7 TGACTGGATTCTCA HLA-DRA            0    SeuratProject        127           56
#>  8 TGACTGGATTCTCA LYZ                0    SeuratProject        127           56
#>  9 AGTCAGACTGCACA HLA-DRA            4.07 SeuratProject        173           53
#> 10 AGTCAGACTGCACA LYZ                0    SeuratProject        173           53
#> # ℹ 150 more rows
#> # ℹ 25 more variables: RNA_snn_res.0.8 <fct>, letter.idents <fct>,
#> #   groups <chr>, RNA_snn_res.1 <fct>, PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>,
#> #   PC_4 <dbl>, PC_5 <dbl>, PC_6 <dbl>, PC_7 <dbl>, PC_8 <dbl>, PC_9 <dbl>,
#> #   PC_10 <dbl>, PC_11 <dbl>, PC_12 <dbl>, PC_13 <dbl>, PC_14 <dbl>,
#> #   PC_15 <dbl>, PC_16 <dbl>, PC_17 <dbl>, PC_18 <dbl>, PC_19 <dbl>,
#> #   tSNE_1 <dbl>, tSNE_2 <dbl>