join_features() extracts and joins information for specific features
# S4 method for class 'SingleCellExperiment'
join_features(
.data,
features = NULL,
all = FALSE,
exclude_zeros = FALSE,
shape = "long",
...
)A tidy SingleCellExperiment object
A vector of feature identifiers to join
If TRUE return all
If TRUE exclude zero values
Format of the returned table "long" or "wide"
Parameters to pass to join wide, i.e. assay name to extract feature abundance from and gene prefix, for shape="wide"
A `tidySingleCellExperiment` object containing information for the specified features.
This function extracts information for specified features and returns the information in either long or wide format.
data(pbmc_small)
pbmc_small %>% join_features(
features=c("HLA-DRA", "LYZ"))
#> tidySingleCellExperiment says: join_features produces duplicate cell names to accomadate the long data format. For this reason, a data frame is returned for independent data analysis. Assay feature abundance is appended as .abundance_counts and .abundance_logcounts.
#> # A tibble: 160 × 34
#> .cell .feature .abundance_counts .abundance_logcounts orig.ident nCount_RNA
#> <chr> <chr> <dbl> <dbl> <fct> <dbl>
#> 1 ATGCCA… HLA-DRA 0 0 SeuratPro… 70
#> 2 ATGCCA… LYZ 1 4.97 SeuratPro… 70
#> 3 CATGGC… HLA-DRA 1 4.78 SeuratPro… 85
#> 4 CATGGC… LYZ 1 4.78 SeuratPro… 85
#> 5 GAACCT… HLA-DRA 0 0 SeuratPro… 87
#> 6 GAACCT… LYZ 1 4.75 SeuratPro… 87
#> 7 TGACTG… HLA-DRA 0 0 SeuratPro… 127
#> 8 TGACTG… LYZ 0 0 SeuratPro… 127
#> 9 AGTCAG… HLA-DRA 1 4.07 SeuratPro… 173
#> 10 AGTCAG… LYZ 0 0 SeuratPro… 173
#> # ℹ 150 more rows
#> # ℹ 28 more variables: nFeature_RNA <int>, RNA_snn_res.0.8 <fct>,
#> # letter.idents <fct>, groups <chr>, RNA_snn_res.1 <fct>, file <chr>,
#> # ident <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>