internalFrequencyTrio_Duo {nanotatoR} | R Documentation |
Calculates the internal frequencies of SV in internal cohorts, for SVMerge
internalFrequencyTrio_Duo( mergedFiles, smappath, smap, buildSVInternalDB = FALSE, smapdata, path, pattern, outpath, win_indel = 10000, win_inv_trans = 50000, perc_similarity = 0.5, indelconf = 0.5, invconf = 0.01, fname, limsize = 1000, win_indel_parents = 5000, win_inv_trans_parents = 40000, transconf = 0.1, dbOutput = c("dataframe", "text"), perc_similarity_parents = 0.9, returnMethod = c("Text", "dataFrame"), input_fmt_SV = c("Text", "dataFrame"), indexfile, EnzymeType = c("SVmerge", "SE"), labelType = c("SVMerge", "SE", "Both"), SVMerge_path, SVMerge_pattern, SE_path, SE_pattern, Samplecodes, mergeKey, mergedKeyoutpath, mergedKeyFname )
mergedFiles |
character. Path to the merged SV files. |
smappath |
character. path to the query smap file. |
smap |
character. File name for the smap |
buildSVInternalDB |
boolean. Checking whether the merged solo file database exist. |
smapdata |
character. Dataframe if input type chosen as dataframe. |
path |
character. Path to the solo file database. |
pattern |
character. pattern of the file names to merge. |
outpath |
character. Path where the merged samples are kept. |
win_indel |
N umeric. Insertion and deletion error window. Default 10000. |
win_inv_trans |
Numeric. Inversion and translocation error window. Default 50000. |
perc_similarity |
Numeric . ThresholdPercentage similarity of the query SV and reference SV. Default 0.5. |
indelconf |
Numeric. Threshold for insertion and deletion confidence. Default 0.5 |
invconf |
Numeric. Threshold for inversion confidence.Default 0.01. |
fname |
character. Filename in case dbOutput = Text. |
limsize |
Numeric. Minimum size of SV that can be determined acurately by the Bionano SV caller. Default 1000. |
win_indel_parents |
Numeric. Insertion and deletion error window to determine zygosity in case of parents. Default 5000. |
win_inv_trans_parents |
Numeric. Inversion and translocation error window to determine zygosity in case of parents. Default 40000. |
transconf |
Numeric. Threshold for translocation confidence. Default 0.1. |
dbOutput |
character. Output of merged bionano data. |
perc_similarity_parents |
Numeric . ThresholdPercentage similarity for zygosity determination. Default 0.9. |
returnMethod |
character. Choice between Text and DataFrame. Required if you want to calculate internal frequency. |
input_fmt_SV |
Format in which data is provided as an input to thefunction. |
indexfile |
File containing connection between sample and nanoIDs |
EnzymeType |
Character. Type of enzyme. Options Dual and DLE. |
labelType |
character. Type of labels used for mapping. Choices are Dual, DLE and Both. |
SVMerge_path |
character. Path for the Dual labelled cmap |
SVMerge_pattern |
character. pattern of the dual files. |
SE_path |
character. Path for the Dual labelled cmap |
SE_pattern |
character. pattern of the dual files. |
Samplecodes |
character. File containing relations and IDs associated to them. |
mergeKey |
character. File containing sample ID and relation. |
mergedKeyoutpath |
character. File path storing sample name and nanoID key information. |
mergedKeyFname |
character. File name storing sample name and nanoID key information. |
Calculated internal frequency in dataframe or text.
smapName="GM24385_Ason_DLE1_VAP_trio5.smap" smap = system.file("extdata", smapName, package="nanotatoR") indelconf = 0.5; invconf = 0.01;transconf = 0.1;input_fmt_SV="Text"; datInf <- internalFrequency_solo( smap = smap, buildSVInternalDB = FALSE, win_indel=10000, win_inv_trans=50000, EnzymeType = "SE", mergedFiles = system.file("extdata", "nanotatoRControl.txt", package="nanotatoR"), perc_similarity_parents =0.9, indexfile = system.file("extdata", "Sample_index.csv", package="nanotatoR"), perc_similarity=0.5, indelconf=0.5, invconf=0.01, transconf=0.1, limsize=1000, win_indel_parents=5000,input_fmt="Text", win_inv_trans_parents=40000, returnMethod="dataFrame", input_fmt_SV = "Text")