fun_read_check {MicroSEC}

Read check function.

Description

This function attempts to check the mutation profile in each read.

Usage

fun_read_check(
  df_mutation,
  df_bam,
  ref_genome,
  sample_name,
  read_length,
  adapter_1,
  adapter_2,
  short_homology_search_length,
  min_homology_search,
  progress_bar
)

Arguments

df_mutation

Mutation information.

df_bam

Data from the BAM file.

ref_genome

Reference genome for the data.

sample_name

Sample name (character)

read_length

The read length in the sequence.

adapter_1

The Read 1 adapter sequence of the library.

adapter_2

The Read 2 adapter sequence of the library.

short_homology_search_length

Small sequence for homology search.

min_homology_search

Minimum length to define "homologous".

progress_bar

"Y": You can see the progress visually.

Value

list(msec, homology_search, mut_depth)

Examples

## Not run: 
data(exampleMutation)
data(exampleBam)
fun_read_check(df_mutation = exampleMutation,
df_bam = exampleBam,
ref_genome = BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38,
sample_name = "sample",
read_length = 150,
adapter_1 = "AGATCGGAAGAGCACACGTCTGAACTCCAGTCA",
adapter_2 = "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT",
short_homology_search_length = 4,
min_homology_search = 40,
progress_bar = "N"
)

## End(Not run)