make_corLong: Create Long Correlation Tables

In LieberInstitute/brainstorm: Validating Sample Identiy Through RNA-seq and DNA Genotyping Correlation

Create Long Correlation Tables

Description

Compute pairwise correlations between one or two snp arrays, then convert to long format

Usage

make_corLong(
  snps1,
  snps2 = snps1,
  BrainTable1,
  BrainTable2 = BrainTable1,
  ID_col1 = "ID",
  ID_col2 = ID_col1
)

Arguments

snps1	Table of snps, RNA or DNA,
snps2	Table of snps, RNA or DNA, if NA snps1 will be compared to its self
BrainTable1	Table containing ID info for samples in snps1
BrainTable2	Table containing ID info for samples in snps2
ID_col1	Name of column containing Samples names in BrainTable1
ID_col2	Name of column containing Samples names in BrainTable2

Value

Data frame with correlation between samples in snps1 (or between snps1 and snps2) and ID info from BrainTables (at least BrNums for samples)

Examples

snpsGeno <- make_snpsGeno(snpsGeno_VCF)
snpsGeno[1:5, 1:5]
corLong <- make_corLong(snpsGeno, BrainTable1 = brain_sentrix)

LieberInstitute/brainstorm documentation built on Dec. 14, 2024, 10:29 p.m.