internalFrequency {nanotatoR} | R Documentation |
Calculates the internal frequencies of SV in internal cohorts
internalFrequency(mergedFiles, smappath, smap, buildSVInternalDB = FALSE, smapdata, input_fmt = c("Text", "dataFrame"), 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"), returnMethod = c("Text", "dataFrame"))
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. |
input_fmt |
Format in which data is provided as an input to the function. |
path |
character. Path to the solo file database. |
pattern |
character. pattern of the file names to merge. |
outpath |
character. Path to merged SV solo datasets. |
win_indel |
Numeric. 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. |
returnMethod |
character. Choice between Text and DataFrame. |
Text file or data frames containing internalFrequency data.
mergedFiles <- system.file("extdata", "nanotatoR_merged.txt", package = "nanotatoR") smapName <- "F1.1_TestSample1_solo_hg19.smap" smappath <- system.file("extdata", package = "nanotatoR") indelconf = 0.5; invconf = 0.01;transconf = 0.1;input_fmt="Text"; internalFrequency(mergedFiles = mergedFiles, smappath = smappath , smap = smapName, buildSVInternalDB=FALSE, win_indel=10000, win_inv_trans=50000, 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")