bc_messyBc.RdmessyBc 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 BarcodeObj
bc_messyBc(barcodeObj, isList = TRUE)A BarcodeObj objects.
A logical value, if TRUE (default), the return is a list with each
sample as an element. Otherwise, the function will return a data.frame
contains the data from all the samples with a column named sample_name
to keep the sample information.
If a list is requested, in the list each element is a
data.frame corresponding to the successive samples. Each
data.frame has at most 3 columns: 1. umi_seq (optional): UMI
sequence. 2. barcode_seq: barcode sequence. 3. count: how many
reads a full sequence has.
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)
#> $test1
#> reads_seq match_seq barcode_seq
#> 1 AATTCGATCGATCGAAGAGATCGATCGATC TCGATCGATCGAAGAGATCGATCGATC AGAG
#> 2 ACTTCGATCGATCGAAAAGATCGATCGATC TCGATCGATCGAAAAGATCGATCGATC AAAG
#> 3 GGATCGATCGATCGAAGAGATCGATCGATC TCGATCGATCGAAGAGATCGATCGATC AGAG
#> 4 AAATCGATCGATCGAAGAGATCGATCGATC TCGATCGATCGAAGAGATCGATCGATC AGAG
#> 5 TTTTCGATCGATCGAAAAGATCGATCGATC TCGATCGATCGAAAAGATCGATCGATC AAAG
#> 6 GGGTCGATCGATCGAAAAGATCGATCGATC TCGATCGATCGAAAAGATCGATCGATC AAAG
#> 7 CCTTCGATCGATCGAAGAAGATCGATCGATC TCGATCGATCGAAGAAGATCGATCGATC AGAAG
#> 8 ACTTCGATCGATCGAACAAGATCGATCGATC TCGATCGATCGAACAAGATCGATCGATC ACAAG
#> 9 CCCTCGATCGATCGAAGAAGATCGATCGATC TCGATCGATCGAAGAAGATCGATCGATC AGAAG
#> 10 GGTTCGATCGATCGACGAGATCGATCGATC TCGATCGATCGACGAGATCGATCGATC CGAG
#> count
#> 1 60
#> 2 30
#> 3 30
#> 4 14
#> 5 10
#> 6 10
#> 7 9
#> 8 6
#> 9 5
#> 10 4
#>
#> $test2
#> reads_seq match_seq barcode_seq
#> 1 ACTTCGATCGATCGAAACGATCGATCGATC TCGATCGATCGAAACGATCGATCGATC AACG
#> 2 GGATCGATCGATCGAAGAGATCGATCGATC TCGATCGATCGAAGAGATCGATCGATC AGAG
#> 3 AAATCGATCGATCGAAGAGATCGATCGATC TCGATCGATCGAAGAGATCGATCGATC AGAG
#> 4 TTTTCGATCGATCGAAAAGATCGATCGATC TCGATCGATCGAAAAGATCGATCGATC AAAG
#> 5 GGGTCGATCGATCGAAAAGATCGATCGATC TCGATCGATCGAAAAGATCGATCGATC AAAG
#> 6 AATTCGATCGATCGAAGAGATCGATCGATC TCGATCGATCGAAGAGATCGATCGATC AGAG
#> 7 ACTTCGATCGATCGAACAAGATCGATCGATC TCGATCGATCGAACAAGATCGATCGATC ACAAG
#> 8 CCCTCGATCGATCGAAGAAGATCGATCGATC TCGATCGATCGAAGAAGATCGATCGATC AGAAG
#> 9 GGTTCGATCGATCGACGAGATCGATCGATC TCGATCGATCGACGAGATCGATCGATC CGAG
#> count
#> 1 30
#> 2 30
#> 3 14
#> 4 10
#> 5 10
#> 6 9
#> 7 6
#> 8 5
#> 9 4
#>
# The return value can be a data.frame
bc_messyBc(bc_obj, isList=FALSE)
#> sample_name reads_seq match_seq
#> 1: test1 AATTCGATCGATCGAAGAGATCGATCGATC TCGATCGATCGAAGAGATCGATCGATC
#> 2: test1 ACTTCGATCGATCGAAAAGATCGATCGATC TCGATCGATCGAAAAGATCGATCGATC
#> 3: test1 GGATCGATCGATCGAAGAGATCGATCGATC TCGATCGATCGAAGAGATCGATCGATC
#> 4: test1 AAATCGATCGATCGAAGAGATCGATCGATC TCGATCGATCGAAGAGATCGATCGATC
#> 5: test1 TTTTCGATCGATCGAAAAGATCGATCGATC TCGATCGATCGAAAAGATCGATCGATC
#> 6: test1 GGGTCGATCGATCGAAAAGATCGATCGATC TCGATCGATCGAAAAGATCGATCGATC
#> 7: test1 CCTTCGATCGATCGAAGAAGATCGATCGATC TCGATCGATCGAAGAAGATCGATCGATC
#> 8: test1 ACTTCGATCGATCGAACAAGATCGATCGATC TCGATCGATCGAACAAGATCGATCGATC
#> 9: test1 CCCTCGATCGATCGAAGAAGATCGATCGATC TCGATCGATCGAAGAAGATCGATCGATC
#> 10: test1 GGTTCGATCGATCGACGAGATCGATCGATC TCGATCGATCGACGAGATCGATCGATC
#> 11: test2 ACTTCGATCGATCGAAACGATCGATCGATC TCGATCGATCGAAACGATCGATCGATC
#> 12: test2 GGATCGATCGATCGAAGAGATCGATCGATC TCGATCGATCGAAGAGATCGATCGATC
#> 13: test2 AAATCGATCGATCGAAGAGATCGATCGATC TCGATCGATCGAAGAGATCGATCGATC
#> 14: test2 TTTTCGATCGATCGAAAAGATCGATCGATC TCGATCGATCGAAAAGATCGATCGATC
#> 15: test2 GGGTCGATCGATCGAAAAGATCGATCGATC TCGATCGATCGAAAAGATCGATCGATC
#> 16: test2 AATTCGATCGATCGAAGAGATCGATCGATC TCGATCGATCGAAGAGATCGATCGATC
#> 17: test2 ACTTCGATCGATCGAACAAGATCGATCGATC TCGATCGATCGAACAAGATCGATCGATC
#> 18: test2 CCCTCGATCGATCGAAGAAGATCGATCGATC TCGATCGATCGAAGAAGATCGATCGATC
#> 19: test2 GGTTCGATCGATCGACGAGATCGATCGATC TCGATCGATCGACGAGATCGATCGATC
#> barcode_seq count
#> 1: AGAG 60
#> 2: AAAG 30
#> 3: AGAG 30
#> 4: AGAG 14
#> 5: AAAG 10
#> 6: AAAG 10
#> 7: AGAAG 9
#> 8: ACAAG 6
#> 9: AGAAG 5
#> 10: CGAG 4
#> 11: AACG 30
#> 12: AGAG 30
#> 13: AGAG 14
#> 14: AAAG 10
#> 15: AAAG 10
#> 16: AGAG 9
#> 17: ACAAG 6
#> 18: AGAAG 5
#> 19: CGAG 4
###