Info on ldpred2.R --help functionality

CHANGELOG.md

@@ -39,6 +39,12 @@ If MD5 sum is not listed for a certain release then it means that the container
 
 * Miscellaneous goes here
 
+## [1.3.5] - 2023-08-17
+
+### Updated
+
+* Updated LDpred2 README file
+
 ## [1.3.4] - 2023-06-22
 
 ### Updated

scripts/pgs/LDpred2/README.md

@@ -15,6 +15,45 @@ This README assumes the following two repositories are cloned using [git](https:
 We also assume the following commands are executed from the current folder
 (the one containing [createBackingFile.R](https://github.com/comorment/containers/blob/main/scripts/pgs/LDpred2/createBackingFile.R) and [ldpred2.R](https://github.com/comorment/containers/blob/main/scripts/pgs/LDpred2/ldpred2.R) scripts).
 
+### Note on help functions
+
+The main R scripts contained in this directory (`ldpred2.R`, `createBackingFile.R`, `imputeGenotypes.R`, `complementSum`) is set up using the [argparser](www.rdocumentation.org/packages/argparser) package for parsing command line arguments.
+The help output from each script can printed to the terminal, issuing:
+
+```
+export SIF=$COMORMENT/containers/singularity
+export RSCRIPT="singularity exec --home=$PWD:/home $SIF/r.sif Rscript"
+# invoke ldpred2.R input options:
+$RSCRIPT ldpred2.R --help
+```
+
+yielding:
+
+```
+usage: ldpred2.R [--] [--help] [--out-merge] [--geno-impute-zero]
+       [--opts OPTS] [--geno-file-rds GENO-FILE-RDS] [--sumstats
+       SUMSTATS] [--out OUT] [--out-merge-ids OUT-MERGE-IDS]
+       [--file-keep-snps FILE-KEEP-SNPS] [--ld-file LD-FILE]
+       [--ld-meta-file LD-META-FILE] [--chr2use CHR2USE] [--col-chr
+       COL-CHR] [--col-snp-id COL-SNP-ID] [--col-A1 COL-A1] [--col-A2
+       COL-A2] [--col-bp COL-BP] [--col-stat COL-STAT] [--col-stat-se
+       COL-STAT-SE] [--col-pvalue COL-PVALUE] [--col-n COL-N]
+       [--stat-type STAT-TYPE] [--effective-sample-size
+       EFFECTIVE-SAMPLE-SIZE] [--n-cases N-CASES] [--n-controls
+       N-CONTROLS] [--name-score NAME-SCORE] [--hyper-p-length
+       HYPER-P-LENGTH] [--hyper-p-max HYPER-P-MAX] [--ldpred-mode
+       LDPRED-MODE] [--cores CORES] [--set-seed SET-SEED]
+       [--merge-by-rsid MERGE-BY-RSID]
+
+Calculate polygenic scores using ldpred2
+
+flags:
+  -h, --help                   show this help message and exit
+  --out-merge                  Merge output with existing file.
+  --geno-impute-zero           Set missing genotypes to zero.
+...
+```
+
 ### Note on filtering of genotype data
 
 The current version of these scripts conduct no filtering of genotype data (e.g., minor allele frequency, imputation quality) prior to calculating linkage disequillibrium or polygenic scores.
@@ -32,7 +71,7 @@ create a copy of the genotypes, thus the imputation performed persists. If you w
 An example use of [imputeGenotypes.R](https://github.com/comorment/containers/blob/main/scripts/pgs/LDpred2/imputeGenotypes.R):
 
 ```
-# Conver from plink format to bigSNPR .rds/.bk files
+# Convert from plink format to bigSNPR .rds/.bk files
 $RSCRIPT createBackingFile.R <fileGeno>.nomiss.bed <fileGeno>.nomiss.rds
 
 # Copy these files if you wish to leave the original files unchanged
@@ -101,6 +140,7 @@ $RSCRIPT calculateLD.R --geno-file-rds $fileGenoRDS \
 ### Effective sample-size
 
 LDpred2 requires information on effective sample-size. There are three ways to provide this to LDpred2:
+
 - As a column in the summary statistics, defaulting to column `N`. If it is a different column, provide with argument `--col-n`.
 - Manually calculated by providing this number with `--effective-sample-size`.
 - Manually specified by providing number of cases and controls with arguments `--n-cases` and `--n-controls`.
@@ -144,6 +184,8 @@ columns of chromosome and position in the `HRC` reference data (default of `--re
 files that are matched. In the example below, output is piped to gzip. To write directly to a file the arguments `--file-output <output file>` and `--file-output-col-sep`
 controls the location of the output file and the column separator used (defaults to tab, "\t").
 
+**_NOTE:_** In case the summary statistics file (or any other file used by the scripts) are outside the working directory, make sure to append its directory to the `SINGULARITY_BIND` environment variable as above, and refer to the file accordingly - otherwise the running container won't see the file.
+
 ### Synthetic example (chr21 and chr22)
 
 The following set of commands gives an example of how to apply LDpred2 on a synthetic example generated [here](https://github.com/comorment/containers/blob/main/scripts/pgs/LDpred2/ldpred2_simulations.ipynb). This only uses chr21 and chr22, so it runs much faster than previous example.

version/version.py

@@ -2,7 +2,7 @@
 _MINOR = "3"
 # On main and in a nightly release the patch should be one ahead of the last
 # released build.
-_PATCH = "4"
+_PATCH = "5"
 # This is mainly for nightly builds which have the suffix ".dev$DATE". See
 # https://semver.org/#is-v123-a-semantic-version for the semantics.
 _SUFFIX = ""