lm_test: Function that will allow for (apply) to be used for linear...

In syyang93/analyzeR: This package contains functions that Stephanie uses for her analysis of recount RNAseq data.

Description

Function that will allow for (apply) to be used for linear regressions This function will do a single linear regression and extract the coefficients from the regression.

Usage

lm_test(lm_data, count, covariates = "", correct_for = "",
  outlier_sd = 3, omit.outlier = T)

Arguments

lm_data	Our dependent variables. Column = dependent variable, rows = observations (in this case, individuals) (numeric vector)
count	Our independent variable (numeric vector)
covariates	Covariates associated with each individual. Columns = covariates, rows = observations. (data.frame)
outlier_sd	Outliers that are greater than outlier_sd standard devs from the mean will be filtered out
to_correct	A string containing additional covariates to correct for. ex: '+as.factor(covariates$DTHHRDY)+as.factor(covariates$RACE)'

Value

Coefficients from the regression

Examples

subcut_lm_results <- apply(subcut_for_test, 2, lm_test, count = MT_count, covariates = covariates, correct_for = '+ as.factor(covariates$GENDER) + as.numeric(covariates$AGE)+ as.numeric(covariates$smrin) + as.factor(covariates$smcenter) + as.factor(covariates$RACE)+ as.numeric(covariates$TRISCHD) +as.factor(covariates$COHORT) + as.factor(covariates$DTHHRDY) + covariates$PC1 + covariates$PC2 +covariates$PC3+ covariates$PC4 + covariates$PC5')

syyang93/analyzeR documentation built on Aug. 26, 2020, 4:34 p.m.