| Title: | Estimation of the science-wise false discovery rate and the false discovery rate conditional on covariates |
|---|---|
| Description: | This package allows users to estimate the science-wise false discovery rate from Jager and Leek, "Empirical estimates suggest most published medical research is true," 2013, Biostatistics, using an EM approach due to the presence of rounding and censoring. It also allows users to estimate the false discovery rate conditional on covariates, using a regression framework, as per Boca and Leek, "A direct approach to estimating false discovery rates conditional on covariates," 2018, PeerJ. |
| Authors: | Jeffrey T. Leek, Leah Jager, Simina M. Boca, Tomasz Konopka |
| Maintainer: | Simina M. Boca <[email protected]>, Jeffrey T. Leek <[email protected]> |
| License: | GPL (>= 3) |
| Version: | 1.31.0 |
| Built: | 2024-09-15 05:32:32 UTC |
| Source: | https://github.com/bioc/swfdr |
A dataset containing 50,000 SNPs and results for their associations with BMI.
data(BMI_GIANT_GWAS_sample)data(BMI_GIANT_GWAS_sample)
A data frame with 50,000 rows and 9 variables:
ID for SNP (single nucleotide polymorphism)
Allele 1 for SNP
Allele 2 for SNP
Frequency of minor allele (MAF) in Hapmap project
Estimated beta for association between SNP and BMI
Estimated standard error (se) for association between SNP and BMI
P-value for association between SNP and BMI
Total sample size considered for association of SNP and BMI
Three approximately equal intervals for the Hapmap MAFs
Object of class tbl_df, tbl, data.frame.
Calculate the science-wise FDR (swfdr)
calculateSwfdr( pValues, truncated, rounded, pi0 = 0.5, alpha = 1, beta = 50, numEmIterations = 100 )calculateSwfdr( pValues, truncated, rounded, pi0 = 0.5, alpha = 1, beta = 50, numEmIterations = 100 )
pValues |
Numerical vector of p-values |
truncated |
Vector of 0s and 1s with indices corresponding to those in pValues; 1 indicates that the p-values is truncated, 0 that it is not truncated |
rounded |
Vector of 0s and 1s with indices corresponding to those in pValues; 1 indicates that the p-values is rounded, 0 that it is not rounded |
pi0 |
Initial prior probability that a hypothesis is null (default is 0.5) |
alpha |
Initial value of parameter alpha from Beta(alpha, beta) true positive distribution (default is 1) |
beta |
Initial value of parameter beta from Beta(alpha, beta) true positive distribution (default is 50) |
numEmIterations |
The number of EM iterations (default is 100) |
pi0 |
Final value of prior probability - estimated from EM - that a hypothesis is null, i.e. estimated swfdr |
alpha |
Final value of parameter alpha - estimated from EM - from Beta(alpha, beta) true positive distribution |
beta |
Final value of parameter beta - estimated from EM - from Beta(alpha, beta) true positive distribution |
z |
Vector of expected values of the indicator of whether the p-value is null or not - estimated from EM - for the non-rounded p-values (values of NA represent the rounded p-values) |
n0 |
Expected number of rounded null p-values - estimated from EM - between certain cutpoints (0.005, 0.015, 0.025, 0.035, 0.045, 0.05) |
n |
Number of rounded p-values between certain cutpoints (0.005, 0.015, 0.025, 0.035, 0.045, 0.05) |
pVals <- runif(100) tt <- rr <- rep(0, 100) resSwfdr <- calculateSwfdr(pValues = pVals, truncated = tt, rounded = rr, numEmIterations=100)pVals <- runif(100) tt <- rr <- rep(0, 100) resSwfdr <- calculateSwfdr(pValues = pVals, truncated = tt, rounded = rr, numEmIterations=100)
Get number of decimals (i.e. return total number of digits after decimal point) for any vector of numbers in [0,1) if number of decimals <= 6
get_number_decimals(x)get_number_decimals(x)
x |
Numerical vector where all elements are in [0,1) |
Vector giving the number of decimals for each element in x if the number is <= 6; otherwise return 7 with a warning
#get_number_decimals(c(0.0006, 0.0750, 0.0420, 0.0031, 0.0001, 0.0100)) #get_number_decimals(c(6*10^-4, 7.5*10^-2, 4.2*10^-2, 3.1*10^-3, 10^-4, 10^-2)) #get_number_decimals(c(6.5*10^-4, 0.0100)) #get_number_decimals(c(6.5e-4, 0.0100)) #get_number_decimals(c(0.00065, 0.0100)) #get_number_decimals(c(10^-7, 10e-7, 10e-3))#get_number_decimals(c(0.0006, 0.0750, 0.0420, 0.0031, 0.0001, 0.0100)) #get_number_decimals(c(6*10^-4, 7.5*10^-2, 4.2*10^-2, 3.1*10^-3, 10^-4, 10^-2)) #get_number_decimals(c(6.5*10^-4, 0.0100)) #get_number_decimals(c(6.5e-4, 0.0100)) #get_number_decimals(c(0.00065, 0.0100)) #get_number_decimals(c(10^-7, 10e-7, 10e-3))
A dataset containing 15,653 p-values.
journals_pValsjournals_pVals
A tbl data frame with 15,653 rows and 5 variables:
P-value
Equals to 1 if the p-value is truncated, 0 otherwise
Pubmed ID of the article
Year of publication
Journal
Object of class tbl_df, tbl, data.frame.
Code for extracting p-values at: inst/script/getPvalues.R
Estimation of pi0, proportion of p-values consistent with a null hypothesis
lm_pi0( p, lambda = seq(0.05, 0.95, 0.05), X, type = c("logistic", "linear"), smooth.df = 3, threshold = TRUE, smoothing = c("unit.spline", "smooth.spline") )lm_pi0( p, lambda = seq(0.05, 0.95, 0.05), X, type = c("logistic", "linear"), smooth.df = 3, threshold = TRUE, smoothing = c("unit.spline", "smooth.spline") )
p |
numeric vector, p-values |
lambda |
numeric vector, thresholds used to bin pvalues, must be in [0,1). |
X |
numeric matrix, covariates that might be related to p values (one test per row, one variable per column). |
type |
character, type of regression used to fit features to pvalues |
smooth.df |
integer, degrees of freedom when estimating pi0(x) with a smoother. |
threshold |
logical, if TRUE, all estimates are thresholded into unit interval; if FALSE, all estimates are left as they are computed |
smoothing |
character, type of smoothing used to fit pi0 |
object of class ‘lm_pi0’, which is a list with several components
call |
matched function call |
lambda |
numeric vector of thresholds used in calculating pi0.lambda |
X.names |
character vector of covariates used in modeling |
pi0.lambda |
numeric matrix of estimated pi0(x) for each value of lambda. The number of columns is the number of tests, the number of rows is the length of lambda. |
pi0 |
numerical vector of smoothed estimate of pi0(x). The length is the number of rows in X. |
pi0.smooth |
(only output with smoothing="smooth.spline") Matrix of fitted values from the smoother fit to the pi0(x) estimates at each value of lambda (same number of rows and columns as pi0.lambda) |
# define a covariate X <- seq(-1,2,length=1000) # set probability of being null pi0 <- 1/4*X + 1/2 # generate null/alternative p-values nullI <- rbinom(1000,prob=pi0,size=1)> 0 # vector of p-values pValues <- rep(NA,1000) pValues[nullI] <- runif(sum(nullI)) # from U(0,1) pValues[!nullI] <- rbeta(sum(!nullI),1,2) # from Beta pi0x <- lm_pi0(pValues, X=X)# define a covariate X <- seq(-1,2,length=1000) # set probability of being null pi0 <- 1/4*X + 1/2 # generate null/alternative p-values nullI <- rbinom(1000,prob=pi0,size=1)> 0 # vector of p-values pValues <- rep(NA,1000) pValues[nullI] <- runif(sum(nullI)) # from U(0,1) pValues[!nullI] <- rbeta(sum(!nullI),1,2) # from Beta pi0x <- lm_pi0(pValues, X=X)
The recipe for turning pvalues into qvalues is adapted from package 'qvalue' and articles by Storey, Tibshirani, Taylor, Siegmund.
lm_qvalue( p, X, pfdr = FALSE, pi0 = NULL, smoothing = c("unit.spline", "smooth.spline"), ... )lm_qvalue( p, X, pfdr = FALSE, pi0 = NULL, smoothing = c("unit.spline", "smooth.spline"), ... )
p |
numeric vector of p-values |
X |
matrix of covariates (can be missing if pi0 is specified instead) |
pfdr |
logical, making estimates robust for small p-values and a small sample size |
pi0 |
list with pi0 estimates from lm_pi0. If this is not provided, pi0 is estimated using function lm_pi0. |
smoothing |
character, type of smoothing used to fit pi0. Note the default in this function is different than in lm_pi0. |
... |
other parameters (passed on to lm_pi0 if pi0 is not provided) |
object of class ‘lm_qvalue’, which is a list with several components
call |
matched function call |
pvalues |
numeric vector of original p-values |
qvalues |
numeric vector of q-values |
|
other list elements transferred from pi0 |
# define a covariate X <- rep(c(0, 1), each=1000) # generate p-values, randomly for group 0 and with low values for group 1 pVal <- c(runif(1000), rbeta(1000, 0.2, 1)) # compute qvalues, using the covariate qVal <- lm_qvalue(pVal, X=X)# define a covariate X <- rep(c(0, 1), each=1000) # generate p-values, randomly for group 0 and with low values for group 1 pVal <- c(runif(1000), rbeta(1000, 0.2, 1)) # compute qvalues, using the covariate qVal <- lm_qvalue(pVal, X=X)