callMetrics: Calculate the metrics of insert size

In cfDNAPro: This Package Helps Characterise and Visualise Whole Genome Sequencing Data from Liquid Biopsy

Description

Calculate the metrics of insert size

Usage

callMetrics(
  path = getwd(),
  groups,
  fun = "all",
  outfmt = "df",
  input_type,
  ...
)

Arguments

path	The root folder containing all groups folders, default is the present working folder.
groups	The name of the groups, the input value should be vector, e.g. groups=c('group1','group2'), default is all sub-folders in the 'path'.
fun	String value, the types of metrics to be calculated. Default is 'all', which means both median and mean values will be returned.
outfmt	The output format, a 'list' or 'dataframe' or 'df', default is dataframe.
input_type	Character. The input file format, should be one of these: 'picard', 'bam'. The bam files has to be marked duplicates.
...	Further arguments passed to or from other methods.

Value

The inter valley distance in list or dataframe format.

Author(s)

Haichao Wang

Examples

# Get the path to example data.
path <- examplePath("groups_picard")
# Calculate the metrics.
df <- callMetrics(path = path)

Example output

Loading required package: magrittr
Registered S3 method overwritten by 'quantmod':
  method            from
  as.zoo.data.frame zoo 
setting default input_type to picard.

cfDNAPro documentation built on Nov. 8, 2020, 6:49 p.m.