callSize: Calculate the insert size metrics (i.e. prop, cdf, 1-cdf) or...

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

Description

Calculate the insert size metrics (i.e. prop, cdf, 1-cdf) or each group

Usage

callSize(path, groups, outfmt, 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 folders in the folder path.
outfmt	The output format, could specify as '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 function returns the insert size metrics of each group in list or dataframe format.

Author(s)

Haichao Wang

Examples

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

Example output

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

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