callPeakDistance {cfDNAPro} | R Documentation |
Calculate the inter-peak distance of insert size
callPeakDistance( path = getwd(), groups, limit, outfmt, summary, mincount, input_type, ... )
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. |
limit |
The insert size range that will be focused on. Default value is 'limit = c(35,135)'. |
outfmt |
The output format, a 'list' or 'dataframe'. Default is dataframe. |
summary |
If TRUE, summarize the output. |
mincount |
The minimum count value of inter-peak distance in the summary. |
input_type |
Character. The input file format, 'picard' or 'bam'. The bam files has to be marked duplicates. |
... |
Further arguments passed to or from other methods. |
The function returns the inter peak distance in list or dataframe format.
Haichao Wang
# Get the path to example data. path <- examplePath("groups_picard") # Calculate the inter-peak distance. df <- callPeakDistance(path = path)