Decipherfrequency {nanotatoR} | R Documentation |
Frequency calculation of variants compared to Decipher.
Decipherfrequency( decipherpath, smap, smap_data, win_indel = 10000, perc_similarity = 0.5, returnMethod = c("Text", "dataFrame"), input_fmt_SV = c("Text", "dataFrame"), EnzymeType = c("SVMerge", "SE"), outpath )
decipherpath |
character. Decipher Text file. |
smap |
character Filepath for smap. |
smap_data |
Dataset containing smap data. |
win_indel |
character indel window. Default 10000. |
perc_similarity |
Numeric . ThresholdPercentage similarity of the query SV and reference SV. |
returnMethod |
character. Choice between text or data frame as the output. |
input_fmt_SV |
boolean . Options SE and SVMerge. |
EnzymeType |
boolean . Options SE and SVMerge. |
outpath |
character. Path where gene lists are saved. |
dataframe containing decipher data. are stored as text files.
decipherpath = system.file("extdata", "population_cnv.txt", package="nanotatoR") smappath=system.file("extdata", "GM24385_Ason_DLE1_VAP_trio5.smap", package="nanotatoR") datdecipher <- Decipherfrequency (decipherpath = decipherpath, smap = smappath, win_indel = 10000, EnzymeType= "SE", perc_similarity = 0.5,returnMethod="dataFrame", input_fmt_SV = "Text") datdecipher[1,]