nanotatoR_main {nanotatoR} | R Documentation |
Annotation of Bionano SV.
nanotatoR_main(smap, bed, inputfmtBed = c("BED", "BNBED"), n = 3, InternalDBpath, InternalDBpattern, dbOutput_Int, fname_Int, dbOutput_BN, fname_BN, buildSVInternalDB = FALSE, soloPath, solopattern, returnMethod_bedcomp = c("Text", "dataFrame"), mergedFiles_BN, win_indel_INF = 10000, win_inv_trans_INF = 50000, perc_similarity_INF = 0.5, indelconf = 0.5, invconf = 0.01, transconf = 0.1, returnMethod_DGV = c("Text", "dataFrame"), hgpath, win_indel_DGV = 10000, win_inv_trans_DGV = 50000, perc_similarity_DGV = 0.5, returnMethod_Internal = c("Text", "dataFrame"), input_fmt_DGV = c("Text", "dataFrame"), input_fmt_BN = c("Text", "dataFrame"), input_fmt_INF = c("Text", "dataFrame"), input_fmt_decipher = c("Text", "dataFrame"), input_fmt_svMap = c("Text", "dataFrame"), dat_geneList, decipherpath, input_fmt_geneList = c("Text", "dataFrame"), returnMethod_GeneList = c("Text", "dataFrame"), buildBNInternalDB = FALSE, returnMethod_BNCohort = c("Text", "dataFrame"), mergedFiles_INF, returnMethod_decipher = c("Text", "dataFrame"), method_entrez = c("Single", "Multiple", "Text"), smapName, termPath, term, thresh = 5, limsize = 1000, win_indel_parents = 5000, win_inv_trans_parents = 40000, outpath, outputFilename = "", RZIPpath)
smap |
character. Path to SMAP file. |
bed |
Text Choice between UCSC bed or Bionano bed. |
inputfmtBed |
character. Choice between Text and DataFrame as input for bed file. |
n |
numeric Number of genes to report which are nearest to the breakpoint. Default is 3. |
InternalDBpath |
character. Path to the BNFile file database. |
InternalDBpattern |
character. pattern of the BNFile names to merge. |
dbOutput_Int |
character. Output of solo bionano data. |
fname_Int |
character. Filename in case dbOutput_Int = Text. |
dbOutput_BN |
character. Output of merged bionano data. |
fname_BN |
character. Filename in case dbOutput_BN = Text. |
buildSVInternalDB |
boolean. Checking whether the merged solo file database exist or you need to build it. Default= TRUE. |
soloPath |
character. Path to the solo file database. |
solopattern |
character. pattern of the file names to merge. |
returnMethod_bedcomp |
character. Return Methods from the compSmapbed function, choice between Text and Dataframe. |
mergedFiles_BN |
character. Path to the merged BN SV files. |
win_indel_INF |
Numeric. Insertion and deletion error window. |
win_inv_trans_INF |
Numeric. Inversion and translocation error window. |
perc_similarity_INF |
Numeric . ThresholdPercentage similarity of the query SV and reference SV. |
indelconf |
Numeric. Threshold for insertion and deletion confidence. |
invconf |
Numeric. Threshold for inversion confidence. |
transconf |
Numeric. Threshold for translocation confidence. |
returnMethod_DGV |
character. Return Methods from the DGV_extraction function, choice between Text and Dataframe. |
hgpath |
character. Path to Database of Genomic Variants (DGV) Text file. |
win_indel_DGV |
Numeric. Insertion and deletion error window. |
win_inv_trans_DGV |
Numeric. Inversion and translocation error window. |
perc_similarity_DGV |
Numeric . ThresholdPercentage similarity of the query SV and reference SV. |
returnMethod_Internal |
character. Return Methods from the internalFrequency function, choice between Text and Dataframe. |
input_fmt_DGV |
character. Choice between Text and DataFrame for input to DGV. |
input_fmt_BN |
character. Choice of Bionano dataset input Text or Dataframe. |
input_fmt_INF |
character. Choice between Text and DataFrame for input to INF. |
input_fmt_decipher |
character. Choice of gene list input Text or Dataframe. |
input_fmt_svMap |
character. Choice of SVmap input for final step Text or Dataframe. |
dat_geneList |
Dataframe Input data containing geneList data. |
decipherpath |
character. Path to DECIPHER. Text file. |
input_fmt_geneList |
character. Choice of gene list input Text or Dataframe. |
returnMethod_GeneList |
character. Return Methods from the gene_list_generation function, choice between Text and Dataframe. |
buildBNInternalDB |
boolean. Checking whether the merged Bionano file database exist or you need to build it. Default= TRUE. |
returnMethod_BNCohort |
character. Return Methods from the Bionano function, choice between Text and Dataframe. |
mergedFiles_INF |
character. Path to the merged BN SV files. |
returnMethod_decipher |
character. Return Methods from the decipher Frequency function, choice between Text and Dataframe. |
method_entrez |
character. Input Method for terms for entrez. Choices are "Single","Multiple" and "Text". |
smapName |
character. Name of the smap file. |
termPath |
character. Path and file name for textfile for terms. |
term |
character. Single or Multiple Terms as vectord. |
thresh |
integer. Threshold for the number of terms sent to entrez. Note if large lists are sent to ncbi, it might fail to get processed. Default is 5. |
limsize |
Numeric. Minimum size of SV that can be determined accurately 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. |
outpath |
Character Directory to the output file. |
outputFilename |
Character Output filename for the annotated smap. |
RZIPpath |
Character. Path for the Rtools zip.exe |
Excel file containing the annotated SV map, tabs divided based on type of SVs.