bc_cure_depth {CellBarcode} | R Documentation |
bc_cure_depth filters barcodes by the read counts or the UMI counts.
bc_cure_depth(barcodeObj, depth = 0, isUpdate = TRUE) ## S4 method for signature 'BarcodeObj' bc_cure_depth(barcodeObj, depth = 0, isUpdate = TRUE)
barcodeObj |
A BarcodeObj object. |
depth |
A numeric or a vector of numeric, specifying the threshold of
minimum count for a barcode to kept. If the input is a vector, if the vector
length is not the same to the sample number the element will be repeatedly
used. And when the depth argument is a number with negative value, automatic
cutoff point will be chosen by |
isUpdate |
A logical value. If TRUE, the |
A BarcodeObj
object with cleanBc
slot updated or
created.
data(bc_obj) d1 <- data.frame( seq = c( "ACTTCGATCGATCGAAAAGATCGATCGATC", "AATTCGATCGATCGAAGAGATCGATCGATC", "CCTTCGATCGATCGAAGAAGATCGATCGATC", "TTTTCGATCGATCGAAAAGATCGATCGATC", "AAATCGATCGATCGAAGAGATCGATCGATC", "CCCTCGATCGATCGAAGAAGATCGATCGATC", "GGGTCGATCGATCGAAAAGATCGATCGATC", "GGATCGATCGATCGAAGAGATCGATCGATC", "ACTTCGATCGATCGAACAAGATCGATCGATC", "GGTTCGATCGATCGACGAGATCGATCGATC", "GCGTCCATCGATCGAAGAAGATCGATCGATC" ), freq = c( 30, 60, 9, 10, 14, 5, 10, 30, 6, 4 , 6 ) ) pattern <- "([ACTG]{3})TCGATCGATCGA([ACTG]+)ATCGATCGATC" bc_obj <- bc_extract(list(test = d1), pattern, sample_name=c("test"), pattern_type=c(UMI=1, barcode=2)) # Remove barcodes with depth < 5 (bc_cured <- bc_cure_depth(bc_obj, depth=5)) bc_2matrix(bc_cured) # Use UMI information, filter the barcode < 5 UMI bc_umi_cured <- bc_cure_umi(bc_obj, depth =0, doFish=TRUE, isUniqueUMI=TRUE) bc_cure_depth(bc_umi_cured, depth = 5) ###