bc_obj: A dummy BarcodeObj object

In wenjie1991/Bc: Cellular DNA Barcode Analysis toolkit

A dummy BarcodeObj object

Description

Dataset contains a BarcodeObj with makeup barcode data.

Usage

data(bc_obj)

Format

This is a BarcodeObj object

Value

A BarcodeObj object.

Source

This is a BarcodeObj object derived from makeup data by:

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
        )
    )

d2 = data.frame(
    seq = c(
       "ACTTCGATCGATCGAAACGATCGATCGATC",
       "AATTCGATCGATCGAAGAGATCGATCGATC",
       "TTTTCGATCGATCGAAAAGATCGATCGATC",
       "AAATCGATCGATCGAAGAGATCGATCGATC",
       "CCCTCGATCGATCGAAGAAGATCGATCGATC",
       "GGGTCGATCGATCGAAAAGATCGATCGATC",
       "GGATCGATCGATCGAAGAGATCGATCGATC",
       "ACTTCGATCGATCGAACAAGATCGATCGATC",
       "GGTTCGATCGATCGACGAGATCGATCGATC",
       "GCGTCCATCGATCGAAGAAGATCGATCGATC"
       ),
    freq = c(
        30, 9, 10, 14, 5, 10, 30, 6, 4 , 6
        )
    )

pattern = "TCGATCGATCGA([ACTG]+)ATCGATCGATC"
bc_obj = bc_extract(
    list(test1 = d1, test2 = d2), 
    pattern, sample_name=c("test1", "test2"))

bc_obj = bc_cure_depth(bc_obj, depth=5)

# Save the dummy data
# save(bc_obj, file = "./data/bc_obj.RData")
###

wenjie1991/Bc documentation built on Aug. 10, 2024, 11:02 a.m.