Description Usage Arguments Value Author(s)
View source: R/functions_main.R
This function will generate a configuration list based on the provided arguments. This list will have the provide in further analysis steps.
1 2 3 4 | AlleleProfileR.setup(samples, genes, index, cutoff = 0.02,
ignore.snp = F, ignore.single = F, ignore.chimeric = F,
cut.range = 0, alternate = NULL, cutoff.large = 25,
chimeric.max.insertion.size = 50, suppress.messages = F)
|
samples |
Table with all samples entries, as generated by AlleleProfileR.read.folders. |
genes |
Path to the .csv file containing all gene entries. |
index |
Path to the .fa file containing the reference genome. |
cutoff |
Percent value (0 to 1), representing the treshold read count for a certain allelic variant to be included in further analysis. |
ignore.snp |
Ignore SNPs? Default is FALSE. |
ignore.single |
Ingore alleles representing a single read pair? Default is FALSE. |
ignore.chimeric |
Ignore chimeric reads? Default is FALSE. |
cut.range |
Range around cut site for considering NHEJ. Default is 0, this setting will disregard cut range. |
alternate |
List of alternate objects for all samples (in order), NULL if not used. |
cutoff.large |
Cutoff value for determining whether an indel is large or small. Default is 25. |
chimeric.max.insertion.size |
Max insertion size when inspecting chemeric alignments. Default is 50. |
suppress.messages |
Suppress messages? Default is FALSE. |
list
Arne Bruyneel
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