filter_data.RdFiltering of spots/cells, genes or samples, as well as count-based filtering
filter_data(
x = NULL,
spot_minreads = 0,
spot_maxreads = NULL,
spot_mingenes = 0,
spot_maxgenes = NULL,
spot_minpct = 0,
spot_maxpct = NULL,
gene_minreads = 0,
gene_maxreads = NULL,
gene_minspots = 0,
gene_maxspots = NULL,
gene_minpct = 0,
gene_maxpct = NULL,
samples = NULL,
rm_tissue = NULL,
rm_spots = NULL,
rm_genes = NULL,
rm_genes_expr = NULL,
spot_pct_expr = "^MT-"
)an STlist
the minimum number of total reads for a spot to be retained
the maximum number of total reads for a spot to be retained
the minimum number of non-zero counts for a spot to be retained
the maximum number of non-zero counts for a spot to be retained
the minimum percentage of counts for features defined by spot_pct_expr for a spot to be retained.
the maximum percentage of counts for features defined by spot_pct_expr for a spot to be retained.
the minimum number of total reads for a gene to be retained
the maximum number of total reads for a gene to be retained
he minimum number of spots with non-zero counts for a gene to be retained
the maximum number of spots with non-zero counts for a gene to be retained
the minimum percentage of spots with non-zero counts for a gene to be retained
the maximum percentage of spots with non-zero counts for a gene to be retained
samples (as in names(x@counts)) to perform filtering.
sample (as in names(x@counts)) to remove from STlist. Removes samples in x@counts, x@tr_counts, x@spatial_meta, x@gene_meta, and x@sample_meta
vector of spot/cell IDs to remove. Removes spots/cells in x@counts, x@tr_counts, and x@spatial_meta
vector of gene names to remove from STlist. Removes genes in x@counts, x@tr_counts, and x@gene_meta
a regular expression that matches genes to remove. Removes genes in x@counts, x@tr_counts, and x@gene_meta
a expression to use with spot_minpct and spot_maxpct. By default '^MT-'.
an STlist containing the filtered data
This function provides options to filter elements in an STlist. It can remove
cells/spots or genes based on raw counts (x@counts). Users can input an
regular expression to query gene names and calculate percentages (for example %
mtDNA genes). The function also can filter entire samples. Note that the function
removes cells/spots, genes, and/or samples in the raw counts, transformed counts,
spatial variables, gene variables, and sample metadata. Also note that the function
filters in the following order:
Samples (rm_tissue)
Spots (rm_spots)
Genes (rm_genes)
Genes matching rm_genes_expr
Min and max counts
# Using included melanoma example (Thrane et al.)
# Download example data set from spatialGE_Data
thrane_tmp = tempdir()
unlink(thrane_tmp, recursive=TRUE)
dir.create(thrane_tmp)
lk='https://github.com/FridleyLab/spatialGE_Data/raw/refs/heads/main/melanoma_thrane.zip?download='
download.file(lk, destfile=paste0(thrane_tmp, '/', 'melanoma_thrane.zip'), mode='wb')
zip_tmp = list.files(thrane_tmp, pattern='melanoma_thrane.zip$', full.names=TRUE)
unzip(zipfile=zip_tmp, exdir=thrane_tmp)
# Generate the file paths to be passed to the STlist function
count_files <- list.files(paste0(thrane_tmp, '/melanoma_thrane'),
full.names=TRUE, pattern='counts')
coord_files <- list.files(paste0(thrane_tmp, '/melanoma_thrane'),
full.names=TRUE, pattern='mapping')
clin_file <- list.files(paste0(thrane_tmp, '/melanoma_thrane'),
full.names=TRUE, pattern='clinical')
# Create STlist
library('spatialGE')
melanoma <- STlist(rnacounts=count_files[c(1,2)],
spotcoords=coord_files[c(1,2)],
samples=clin_file) # Only first two samples
#> Warning: Sample ST_mel3_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!
melanoma <- filter_data(melanoma, spot_minreads=2000)