bc_messyBc {CellBarcode} | R Documentation |
messyBc
slot of BarcodeObj object contains the raw barcode reads
frequency data. For more detail about the messyBc
slot, see
BarcodeObj
. bc_messyBc
is used to access
the 'messyBc' slot in the BarcodeObj
.
bc_messyBc(barcodeObj, isList = TRUE) ## S4 method for signature 'BarcodeObj' bc_messyBc(barcodeObj, isList = TRUE)
barcodeObj |
A |
isList |
A logical value, if TRUE (default), the return is a list with each
sample as an element. Otherwise, the function will return a |
If a list
is requested, in the list
each element is a
data.frame
corresponding to the successive samples. Each
data.frame
has 5 columns: 1. reads_seq
: full read sequence
before parsing. 2. match_seq
: the sequence matched by pattern given to
bc_extract
. 3. umi_seq
(optional): UMI sequence. 4.
barcode_seq
: barcode sequence. 5. count
: how many reads a full
sequence has. In this table, barcode_seq
value can be duplicated, as
two different full read sequences can contain the same barcode sequence, due
to the diversity of the UMI or mutations in the constant region.
#' If a data.frame
is requested, the data.frame
in the list
described above are combined into one data.frame
by row, with an extra
column named sample_name
for identifying sample.
data(bc_obj) # get the data in messyBc slot # default the return value is a list bc_messyBc(bc_obj) # the return value can be a data.frame bc_messyBc(bc_obj, isList=FALSE) ###