get_source_idx: Gets bedgraph column indexes from common pipeline output...
In CompEpigen/scMethrix: Fast and efficient summarization of single cell whole genome bisulfate data
Description
Usage
Arguments
Details
Value
Examples
View source: R/accessory_funcs.R
Description
Gets bedgraph column indexes from common pipeline output formats
Usage
1
2
3
4
get_source_idx(
protocol = c("Bismark_cov", "MethylDackel", "MethylcTools", "BisSNP",
"BSseeker2_CGmap")
)
Arguments
protocol
string; the protocol used for bedgraph output. Options are: "Bismark_cov", "MethylDackel", "MethylcTools", "BisSNP", "BSseeker2_CGmap"
Details
Typically used to reduce the number of potential CpG sites to include only those present in the input files so as to maximize performance and minimize resources. Can also be used for quality control to see if there is excessive number of CpG sites that are not present in the reference genome.
Value
List of column names and indexes
Examples
1
get_source_idx("MethylDackel")
CompEpigen/scMethrix documentation built on Nov. 6, 2021, 3:09 p.m.
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Description Usage Arguments Details Value Examples
View source: R/accessory_funcs.R
Description
Gets bedgraph column indexes from common pipeline output formats
Usage
1 2 3 4 | get_source_idx(
protocol = c("Bismark_cov", "MethylDackel", "MethylcTools", "BisSNP",
"BSseeker2_CGmap")
)
|
Arguments
protocol |
string; the protocol used for bedgraph output. Options are: "Bismark_cov", "MethylDackel", "MethylcTools", "BisSNP", "BSseeker2_CGmap" |
Details
Typically used to reduce the number of potential CpG sites to include only those present in the input files so as to maximize performance and minimize resources. Can also be used for quality control to see if there is excessive number of CpG sites that are not present in the reference genome.
Value
List of column names and indexes
Examples
1 | get_source_idx("MethylDackel")
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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