inst/extdata/README.md

In yannchristinat/oncoscanR: Secondary analyses of CNV data (HRD and more)

File chas_example.txt

Toy example containing a subset of the alterations of a real ChAS export file.

File ascat_example.txt

Toy example containing a subset of the alterations of a ASCAT result file.

File OncoScan_CNV.na33.r2.annot.processed.bed

Arm coverage of the Oncoscan na33.r2 assay. Of note, the arms 13p, 14p, 15p, 21p and 22p are not covered by the Oncoscan.

Source

References downloaded from the ThermoFisher website: OncoScan_CNV_Analysis_Files_NA33.r5.zip. Then the position of each probe was extracted from the SQLite database (OncoScan_CNV.na33.r2.annot.db file) with the following command:

SELECT Chr_id, Start, Stop, Cytoband, dbSNP_RS_ID, ProbeSet_ID FROM Annotations WHERE Process_Flag > 0;

Data was then saved in a temporary file (sql-output.csv) and processed to group probes based on their distance to the next probe (different groups if more than 300Kbp, the genome-wide Oncoscan resolution). Groups with less than 10 probes and situated at the ends of the chromosome or close to the centromere were discarded.

Grouping procedure in python3:

snp = dict()
with open('sql-output.csv', 'r') as f:
    h = f.readline()  # skip headers
    for l in f:
        toks = l.strip().split('\t')
        arm = toks[0] + toks[3][0]
        pos = int(toks[1])
        if arm not in snp:
            snp[arm] = []
        snp[arm].append(pos)

for arm in sorted(snp.keys()):
    snps = sorted(snp[arm])
    start = {'pos': snps[0], 'i':0}
    for i in range(len(snps)-1):
        if snps[i+1]-snps[i] > 300000:
            print('\t'.join([arm, str(start['pos']), str(snps[i]),
                             str(i+1-start['i']),
                             str((snps[i]-start['pos'])/1000)]))
            start = {'pos': snps[i+1], 'i': i+1}
    print('\t'.join([arm, str(start['pos']), str(snps[-1]),
                     str(len(snps)+1-start['i']),
                     str((snps[-1]-start['pos'])/1000)]))

The output of the python script was saved in the file OncoScan_CNV.na33.r2.annot.processed.bed

Format

A BED file with 3 columns (chromosome, start, end) and one line for each arm.

File LST_gene_list_full_location.txt

A ChAS export file of a tumor sample with an HR-deficient phenotype

File TDplus_gene_list_full_location.txt

A ChAS export file of a tumor sample with a CDK12-mutated phenotype

File triploide_gene_list_full_location.txt

A ChAS export file of a sample with a triploid tumor

yannchristinat/oncoscanR documentation built on Oct. 27, 2023, 11:19 p.m.