LogRcorrection

GC correction file creation

The script createGCcontentFile.R can help you create the input for ASCAT’s GC correction for any platform (both array and sequencing data). Please note that this can be quite CPU/memory intensive so should be run on a HPC. R dependencies: doParallel, foreach and Biostrings.

Rscript createGCcontentFile.R SNPpos CORES REF

• SNPpos should contain the list of all probes with their genomic location (tab-separated).

	Chr	Position
rs3094315	1	752566
rs2073813	1	753541
rs2905040	1	770216
rs12124819	1	776546
rs2980314	1	781258

• CORES defines how many cores to use for the computation.
• REF should be the path to your local reference genome. Make sure that chromosome names in SNPpos fit with REF (e.g. chr1 is different from 1). Please note that sequence must be A/C/G/T/N-based (some references contain lowercase letters for specific regions such as repetitive sequences).

The created output file (GCcontent_SNPloci.txt) should start like this, with one row per provided probe:

	Chr	Position	25bp	50bp	100bp	200bp	500bp	1kb	2kb	5kb	10kb	20kb	50kb	100kb	200kb	500kb	1Mb
rs3094315	1	752566	0.4	0.431373	0.366337	0.363184	0.40519	0.435564	0.428286	0.431314	0.444656	0.427279	0.434511	0.444756	0.462163	0.502001	0.517332
rs2073813	1	753541	0.6	0.490196	0.514851	0.487562	0.499002	0.484515	0.496752	0.441512	0.460054	0.439778	0.437291	0.444906	0.463808	0.50239	0.517472
rs2905040	1	770216	0.24	0.313725	0.306931	0.348259	0.46507	0.483516	0.517741	0.491502	0.466453	0.468427	0.453431	0.441786	0.474883	0.508137	0.522142
rs12124819	1	776546	0.36	0.392157	0.376238	0.39801	0.431138	0.452547	0.437781	0.44891	0.464254	0.463777	0.465511	0.445236	0.481648	0.510419	0.523123
rs2980314	1	781258	0.6	0.568627	0.544554	0.527363	0.433134	0.431568	0.435282	0.462507	0.471153	0.460927	0.467091	0.444976	0.486573	0.510809	0.52383

Replication timing correction file creation

The R script createReplicTimingfile.R can help you create the optional replication timing input for ASCAT’s wave correction for any platform (both array and sequencing data). R dependency: rtracklayer.

Rscript createReplicTimingFile.R SNPpos

• SNPpos is the same file provided to generate the GC correction file above. Please note that chromosomes names for replication timing data are 1, 2, etc. (not chr1, chr2, etc.).

The created output file (ReplicationTiming_SNPloci.txt) should start like this, with one row per provided probe:

	Chr	Position	Bg02es	Bj	Gm06990	Gm12801	Gm12812	Gm12813	Gm12878	Helas3	Hepg2	Huvec	Imr90	K562	Mcf7	Nhek	Sknsh
rs3094315	1	752566	54.905624	60.098045	58.936962	60.200775	59.797001	57.530655	61.163361	63.059586	68.468796	58.805431	67.670982	67.934761	64.411995	57.198978	58.010719
rs2073813	1	753541	54.966686	60.175228	58.960648	60.191437	59.853878	57.569115	61.162411	63.085983	68.470589	58.821083	67.701759	67.995796	64.448158	57.264729	57.990158
rs2905040	1	770216	56.000576	61.533062	59.517155	60.315243	60.879486	58.433681	61.421215	63.689762	68.565933	59.307125	68.349823	69.068848	65.135139	58.516354	57.936165
rs12124819	1	776546	56.495754	62.174568	59.858677	60.523235	61.383484	58.944229	61.69376	64.059311	68.656227	59.664303	68.723213	69.572342	65.509315	59.173409	58.08889
rs2980314	1	781258	56.79295	62.546955	60.079067	60.68153	61.683388	59.267509	61.892082	64.298447	68.724228	59.908783	68.960464	69.863716	65.745972	59.575733	58.227413

Please note that replication timing information comes from ENCODE and is based on hg19. Therefore, script will only works on hg19/GRCh37 SNPs due to the lack of publicly available replication data on other genomes like hg38. However, one may lift-over hg38/GRCh38 loci to hg19/GRCh37 coordinates, extract replication timing information and reset coordinates back to hg38/GRCh38.

Additional information

Please note that row names in the SNPpos file need to be unique but don't need to be SNP IDs (e.g. from dbSNP). One can define row names as ${chromosome}_${position} as long as they are unique and match with row names in logR/BAF files. See our GC correction file for WGS (under ReferenceFiles/WGS).