examine_symbol: Gets the adjusted variable plot for mtDNA vs transcripts for...

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

Description

Gets the adjusted variable plot for mtDNA vs transcripts for people who remain after filtering

Usage

examine_symbol(lm_data, symbol, gene_key, omit.outlier = T,
  correct_for = "as.factor(lm_data$SEX) + as.numeric(lm_data$AGE) + as.numeric(lm_data$RACE) +\n                  lm_data$PC1 + lm_data$PC2 + lm_data$PC3 + lm_data$PC4 + lm_data$PC5 + lm_data$PC6 + lm_data$PC7 + lm_data$PC8 + lm_data$PC9 + lm_data$PC10 + lm_data$Genotyping.PC1 + lm_data$Genotyping.PC2 + lm_data$Genotyping.PC3",
  col = NA)

Arguments

lm_data	lm_full you want to examine the transcript in
symbol	a string with the gene symbol you want to look at
gene_key	a gene key with symbol -> transcript information (tpms_gene_key.rds)
omit.outlier	T/F whether you want to omit outliers > 3SD away from the mean
correct_for	a string that says what you need to correct transcripts for
col	A string, what you want to color the adjusted variable plot with

Value

Transcripts for those individuals

Examples

examine_symbol(blood_full, 'POLG', omit.outlier = T, correct_for = 'as.factor(lm_data$SEX)', col = 'esoph_day')

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