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[Update] Help messages
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@choishingwan
choishingwan committed May 18, 2020
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121 changes: 67 additions & 54 deletions PRSice.R
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ In_Regression <-
R2 <-
print.p <- R <- P <- value <- Phenotype <- Set <- PRS.R2 <- LCI <- UCI <- quant.ref <- NULL

r.version <- "2.2.14"
r.version <- "2.3.0"
# Help Messages --------------------------------------
help_message <-
"usage: Rscript PRSice.R [options] <-b base_file> <-t target_file> <--prsice prsice_location>\n
Expand All @@ -28,11 +28,18 @@ help_message <-
--dir Location to install ggplot. Only require if ggplot\n
is not installed\n
\nBase File:\n
--A1 Column header containing allele 1 (effective allele)\n
Default: A1\n
--A2 Column header containing allele 2 (non-effective allele)\n
Default: A2\n
--base | -b Base association file\n
--base-info Base INFO score filtering. Format should be\n
<Column name>:<Threshold>. SNPs with info \n
score less than <Threshold> will be ignored\n
Column name default: INFO\n
Threshold default: 0.9\n
--base-maf Base MAF filtering. Format should be\n
<Column name>:<Threshold>. SNPs with maf\n
less than <Threshold> will be ignored. An\n
additional column can also be added (e.g.\n
also filter MAF for cases), using the\n
following format:\n
<Column name>:<Threshold>,<Column name>:<Threshold>\n
--beta Whether the test statistic is in the form of \n
BETA or OR. If set, test statistic is assume\n
to be in the form of BETA. Mutually exclusive\n
Expand All @@ -41,25 +48,13 @@ help_message <-
Default: BP\n
--chr Column header containing the chromosome\n
Default: CHR\n
--index If set, assume the INDEX instead of NAME for\n
--index If set, assume the INDEX instead of NAME for\n
the corresponding columns are provided. Index\n
should be 0-based (start counting from 0)\n
--base-info Base INFO score filtering. Format should be\n
<Column name>,<Threshold>. SNPs with info \n
score less than <Threshold> will be ignored\n
Column name default: INFO\n
Threshold default: 0.9\n
--base-maf Base MAF filtering. Format should be\n
<Column name>,<Threshold>. SNPs with maf\n
less than <Threshold> will be ignored. An\n
additional column can also be added (e.g.\n
also filter MAF for cases), using the\n
following format:\n
<Column name>,<Threshold>:<Column name>,<Threshold>\n
--no-default Remove all default options. If set, PRSice\n
will not set any default column name and you\n
will have to ensure all required columns are\n
provided. (--snp, --stat, --A1, --pvalue)\n
must manually provide all required columns\n
(--snp, --stat, --A1, --pvalue)\n
--or Whether the test statistic is in the form of \n
BETA or OR. If set, test statistic is assume\n
to be in the form of OR. Mutually exclusive \n
Expand Down Expand Up @@ -103,8 +98,7 @@ help_message <-
will adjust the ascertainment bias of the R2.\n
Note that when multiple binary trait is found,\n
prevalence information must be provided for\n
all of them (Either adjust all binary traits,\n
or don't adjust at all)\n
all of them\n
--remove File containing the sample(s) to be removed from\n
the target file. First column should be FID and\n
the second column should be IID. If --ignore-fid is\n
Expand Down Expand Up @@ -137,11 +131,11 @@ help_message <-
Default is to use dosage instead of hard coding\n
\nClumping:\n
--clump-kb The distance for clumping in kb\n
Default: 250 \n
Default: 250kb (1mb for PRSet)\n
--clump-r2 The R2 threshold for clumping\n
Default: 0.1 \n
Default: 0.1\n
--clump-p The p-value threshold use for clumping.\n
Default: 1.0 \n
Default: 1\n
--ld | -L LD reference file. Use for LD calculation. If not\n
provided, will use the post-filtered target genotype\n
for LD calculation. Support multiple chromosome input\n
Expand Down Expand Up @@ -204,8 +198,8 @@ help_message <-
--no-full By default, PRSice will include the full model, \n
i.e. p-value threshold = 1. Setting this flag will\n
disable that behaviour\n
--interval | -i The step size of the threshold. Default: 0.00005 \n
--lower | -l The starting p-value threshold. Default: 5e-08 \n
--interval | -i The step size of the threshold. Default: 0.00005\n
--lower | -l The starting p-value threshold. Default: 5e-8\n
--model Genetic model use for regression. The genetic\n
encoding is based on the base data where the\n
encoding represent number of the coding allele\n
Expand All @@ -214,25 +208,25 @@ help_message <-
dom - Dominant model, code as 0/1/1\n
rec - Recessive model, code as 0/0/1\n
het - Heterozygous only model, code as 0/1/0\n
--no-regress Do not perform the regression analysis and simply\n
output all PRS.\n
--missing Method to handle missing genotypes. By default, \n
final scores are averages of valid per-allele \n
scores with missing genotypes contribute an amount\n
proportional to imputed allele frequency. To throw\n
out missing observations instead (decreasing the\n
denominator in the final average when this happens),\n
use the 'no_mean_imputation' modifier. Alternatively,\n
you can use the 'center' modifier to shift all scores\n
use the 'SET_ZERO' modifier. Alternatively,\n
you can use the 'CENTER' modifier to shift all scores\n
to mean zero. \n
--no-regress Do not perform the regression analysis and simply\n
output all PRS.\n
--score Method to calculate the polygenic score.\n
Available methods include:\n
avg - Take the average effect size (default)\n
std - Standardize the effect size \n
avg - Take the average effect size (default)\n
std - Standardize the effect size \n
con-std - Standardize the effect size using mean \n
and sd derived from control samples\n
sum - Direct summation of the effect size \n
--upper | -u The final p-value threshold. Default: 0.5 \n
sum - Direct summation of the effect size \n
--upper | -u The final p-value threshold. Default: 0.5\n
\nPRSet:\n
--background String to indicate a background file. This string\n
should have the format of Name:Type where type can be\n
Expand All @@ -258,10 +252,11 @@ help_message <-
can be provided using \n
--snp-set File:Name\n
MSigDB format - Each row represent a single SNP \n
set with the first column containing\n
the name of the SNP set.\n
set with the first column \n
containing the name of the SNP\n
set.\n
--wind-3 Add N base(s) to the 3' region of each feature(s) \n
--wind-5 Add N base(s) to the 5' region of each feature(s) \n
--wind-5 Add N base(s) to the 5' region of each feature(s) \n
\nPlotting:\n
--bar-col-high Colour of the most predicting threshold\n
Default: firebrick\n
Expand All @@ -287,47 +282,62 @@ help_message <-
contain FID if --ignore-fid isn't set.\n
--quant-ref Reference quantile for quantile plot\n
--scatter-r2 y-axis of the high resolution scatter plot should be R2\n
\nMisc:\n
--all-score Output PRS for ALL threshold. WARNING: This\n
will generate a huge file\n
--chr-id Try to construct an RS ID for SNP based on its\n
chromosome, coordinate, effective allele and \n
non-effective allele.\n
e.g. c:L-aBd is translated to: \n
<chr>:<coordinate>-<effective><noneffective>d\n
This is always true for target file, whereas for\n
base file, this is only used if the RS ID \n
wasn't provided\n
--exclude File contains SNPs to be excluded from the\n
analysis\n
--extract File contains SNPs to be included in the \n
analysis\n
--keep-ambig Keep ambiguous SNPs. Only use this option\n
if you are certain that the base and target\n
has the same A1 and A2 alleles\n
--flip-ambig Force flipping of ambiguous SNPs when they are kept.\n
Will also set the --keep-ambig flag\n
--id-delim This parameter causes sample IDs to be parsed as\n
<FID><delimiter><IID>; the default delimiter\n
is '_'. \n
--ignore-fid Ignore FID for all input. When this is set,\n
first column of all file will be assume to\n
be IID instead of FID\n
--memory Maximum memory usage allowed. PRSice will try\n
its best to honor this setting\n
--non-cumulate Calculate non-cumulative PRS. PRS will be reset\n
to 0 for each new P-value threshold instead of\n
adding up\n
--keep-ambig Keep ambiguous SNPs. Only use this option\n
if you are certain that the base and target\n
has the same A1 and A2 alleles\n
--logit-perm When performing permutation, still use logistic\n
regression instead of linear regression. This\n
will substantially slow down PRSice\n
--no-install Forbid PRSice from automatically installing\n
the required packages (e.g. ggplot2)\n
--memory Maximum memory usage allowed (in Mb). PRSice will try\n
its best to honor this setting\n
--non-cumulate Calculate non-cumulative PRS. PRS will be reset\n
to 0 for each new P-value threshold instead of\n
adding up\n
--out | -o Prefix for all file output\n
--perm Number of permutation to perform. This swill\n
generate the empirical p-value. Recommend to\n
use value larger than 10,000\n
--print-snp Print all SNPs used to construct the best PRS\n
--print-snp Print all SNPs that remains in the analysis \n
after clumping is performed. For PRSet, Y \n
indicate the SNPs falls within the gene set \n
of interest and N otherwise. If only PRSice \n
is performed, a single \"gene set\" called \n
\"Base\" will be presented with all entries\n
marked as Y\n
--seed | -s Seed used for permutation. If not provided,\n
system time will be used as seed. When same\n
seed and same input is provided, same result\n
can be generated\n
--thread | -n Number of thread use\n
--use-ref-maf When specified, missingness imputation will be\n
performed based on the reference samples\n
--ultra Ultra aggressive memory usage. When this is enabled\n
PRSice and PRSet will try to load all genotypes into\n
memory after clumping is performed. This should\n
drastically speed up PRSice and PRSet at the expense\n
of higher memory consumption.\n
Has no effect for dosage score\n
--x-range Range of SNPs to be excluded from the whole\n
analysis. It can either be a single bed file\n
or a comma seperated list of range. Range must\n
Expand Down Expand Up @@ -534,6 +544,8 @@ option_list <- list(
make_option(c("--snp-set"), type = "character", dest = "snp_set"),
# Misc
make_option(c("--all-score"), action = "store_true", dest = "all_score"),
make_option(c("--ultra"), action = "store_true"),
make_option(c("--chr-id"), type = "character", dest = "chr_id"),
make_option(c("--exclude"), type = "character"),
make_option(c("--extract"), type = "character"),
make_option(c("--enable-mmap"), action = "store_true", dest = "enable_mmap"),
Expand Down Expand Up @@ -704,7 +716,8 @@ flags <-
"non-cumulate",
"or",
"print-snp",
"use-ref-maf"
"use-ref-maf",
"ultra"
)
# Skip PRSice core function if only plotting is requirec
if (!provided("plot", argv)) {
Expand Down
25 changes: 19 additions & 6 deletions helpers/help_messages.txt
View file
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ m_help_message =
" score less than <Threshold> will be ignored\n"
" Column name default: INFO\n"
" Threshold default: 0.9\n"
" --base-maf Base MAF filtering. Format should be\n"
" --base-maf Base MAF filtering. Format should be\n"
" <Column name>:<Threshold>. SNPs with maf\n"
" less than <Threshold> will be ignored. An\n"
" additional column can also be added (e.g.\n"
Expand All @@ -27,13 +27,13 @@ m_help_message =
" Default: BP\n"
" --chr Column header containing the chromosome\n"
" Default: CHR\n"
" --index If set, assume the INDEX instead of NAME for\n"
" --index If set, assume the INDEX instead of NAME for\n"
" the corresponding columns are provided. Index\n"
" should be 0-based (start counting from 0)\n"
" --no-default Remove all default options. If set, PRSice\n"
" will not set any default column name and you\n"
" will have to ensure all required columns are\n"
" provided. (--snp, --stat, --A1, --pvalue)\n"
" must manually provide all required columns\n"
" (--snp, --stat, --A1, --pvalue)\n"
" --or Whether the test statistic is in the form of \n"
" BETA or OR. If set, test statistic is assume\n"
" to be in the form of OR. Mutually exclusive \n"
Expand Down Expand Up @@ -78,8 +78,7 @@ m_help_message =
" will adjust the ascertainment bias of the R2.\n"
" Note that when multiple binary trait is found,\n"
" prevalence information must be provided for\n"
" all of them (Either adjust all binary traits,\n"
" or don't adjust at all)\n"
" all of them\n"
" --remove File containing the sample(s) to be removed from\n"
" the target file. First column should be FID and\n"
" the second column should be IID. If --ignore-fid is\n"
Expand Down Expand Up @@ -246,6 +245,14 @@ m_help_message =
"\nMisc:\n"
" --all-score Output PRS for ALL threshold. WARNING: This\n"
" will generate a huge file\n"
" --chr-id Try to construct an RS ID for SNP based on its\n"
" chromosome, coordinate, effective allele and \n"
" non-effective allele.\n"
" e.g. c:L-aBd is translated to: \n"
" <chr>:<coordinate>-<effective><noneffective>d\n"
" This is always true for target file, whereas for\n"
" base file, this is only used if the RS ID \n"
" wasn't provided\n"
" --exclude File contains SNPs to be excluded from the\n"
" analysis\n"
" --extract File contains SNPs to be included in the \n"
Expand Down Expand Up @@ -285,6 +292,12 @@ m_help_message =
" --thread | -n Number of thread use\n"
" --use-ref-maf When specified, missingness imputation will be\n"
" performed based on the reference samples\n"
" --ultra Ultra aggressive memory usage. When this is enabled\n"
" PRSice and PRSet will try to load all genotypes into\n"
" memory after clumping is performed. This should\n"
" drastically speed up PRSice and PRSet at the expense\n"
" of higher memory consumption.\n"
" Has no effect for dosage score\n"
" --x-range Range of SNPs to be excluded from the whole\n"
" analysis. It can either be a single bed file\n"
" or a comma seperated list of range. Range must\n"
Expand Down
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