summarize_STlist: Generates a data frame with summary statistics

Produces a data frame with counts per gene and counts per ROI/spot/cell

summarize_STlist(x = NULL)

Arguments

x

an STlist

Value

a data frame

Details

The function creates a table with counts per gene and counts per region of interest (ROI), spot, or cell in the samples stored in the STlist

Examples

# Using included melanoma example (Thrane et al.)
library('spatialGE')
data_files <- list.files(system.file("extdata", package="spatialGE"), recursive=T, full.names=T)
count_files <- grep("counts", data_files, value=T)
coord_files <- grep("mapping", data_files, value=T)
clin_file <- grep("thrane_clinical", data_files, value=T)
melanoma <- STlist(rnacounts=count_files[c(1,2)], spotcoords=coord_files[c(1,2)], samples=clin_file) # Only first two samples
#> Warning: Sample ST_mel2_rep1 was not found among the count/coordinate files.
#> Warning: Sample ST_mel2_rep2 was not found among the count/coordinate files.
#> Warning: Sample ST_mel3_rep1 was not found among the count/coordinate files.
#> Warning: Sample ST_mel3_rep2 was not found among the count/coordinate files.
#> Warning: Sample ST_mel4_rep1 was not found among the count/coordinate files.
#> Warning: Sample ST_mel4_rep2 was not found among the count/coordinate files.
#> Found matrix data
#> Matching gene expression and coordinate data...
#> Converting counts to sparse matrices
#> Completed STlist!
#> 
summarize_STlist(melanoma)
#> # A tibble: 2 × 9
#>   sample_name  spotscells genes min_co…¹ mean_…² max_c…³ min_g…⁴ mean_…⁵ max_g…⁶
#>   <chr>             <int> <int>    <dbl>   <dbl>   <dbl>   <int>   <dbl>   <int>
#> 1 ST_mel1_rep1        279 15666      185   4449.   26687     167   1999.    6441
#> 2 ST_mel1_rep2        293 16148        6   6056.   22682       6   2443.    6009
#> # … with abbreviated variable names ¹​min_counts_per_spotcell,
#> #   ²​mean_counts_per_spotcell, ³​max_counts_per_spotcell,
#> #   ⁴​min_genes_per_spotcell, ⁵​mean_genes_per_spotcell, ⁶​max_genes_per_spotcell