BNDBfrequency {nanotatoR} | R Documentation |
Calculates the internal frequencies of BNDB cohorts
BNDBfrequency( internalBNDB, smappath, smap, buildBNInternalDB = FALSE, smapdata, input_fmt_SV = c("Text", "dataFrame"), dbOutput = c("dataframe", "text"), BNDBpath, BNDBpattern, outpath, win_indel = 10000, win_inv_trans = 50000, perc_similarity = 0.5, indelconf = 0.5, invconf = 0.01, limsize = 1000, transconf = 0.1, returnMethod = c("Text", "dataFrame"), EnzymeType = c("SVmerge", "SE") )
internalBNDB |
character. Path to the merged SV files. |
smappath |
character. path to the query smap file. |
smap |
character. File name for the smap |
buildBNInternalDB |
boolean. Checking whether the merged BNDB file database exist. |
smapdata |
dataframe. smapdata in the form of dataframe. |
input_fmt_SV |
character. Choice between Text and DataFrame. |
dbOutput |
character. database output type. Options dataframe or text. |
BNDBpath |
character. Path to the BNDB file database. |
BNDBpattern |
character. pattern of the file names to merge. |
outpath |
character. Path to merged SV solo datasets. |
win_indel |
Numeric. Insertion and deletion error window. |
win_inv_trans |
Numeric. Inversion and translocation error window. |
perc_similarity |
Numeric . ThresholdPercentage similarity of the query SV and reference SV. |
indelconf |
Numeric. Threshold for insertion and deletion Score. |
invconf |
Numeric. Threshold for inversion Score. |
limsize |
Numeric. SV size limit. |
transconf |
Numeric. Threshold for translocation Score. |
returnMethod |
character. Choice between Text and DataFrame. |
EnzymeType |
Character. Type of enzyme. Options SVmerge and SE. |
Text file or data frames containing internalFrequency data.
path <- system.file("extdata", "Bionano_config/", package = "nanotatoR") pattern <- "*_hg19_*" smapName="GM24385_Ason_DLE1_VAP_trio5.smap" smap = system.file("extdata", smapName, package="nanotatoR") BNDBfrequency(smap = smap, buildBNInternalDB=TRUE, input_fmt_SV = "Text", dbOutput="dataframe", BNDBpath = path, BNDBpattern = pattern, outpath, win_indel = 10000, win_inv_trans = 50000, perc_similarity = 0.5, indelconf = 0.5, invconf = 0.01, limsize = 1000, transconf = 0.1, returnMethod=c("dataFrame"), EnzymeType = c("SE"))