GDD: Re-structurize the input data

In JingXieMIZZOU/BLMRM: A Bayesian Logistic Regression Model for Genome-Wide Detection of Allele-Specific Gene Expression

Description

A function to convert the raw data into a structure which contains necessary information for analysis, i.e., SNPs, Replicates, counts from maternal allel (YI) and total counts (NI). This structure is friendly to GLMM fitting in glmer() function in "lme4" package. This function can be easily modified to apply to other similar real data structures.

Usage

GDD(i, data, rep)

Arguments

i	The gene number of each gene. Take the sample dataset for instance, the gene number of the first gene in this dataset is 28.
data	The raw data, need to be in the exact format with the sample data provided by this package, more specifically, a data.frame with its first 3 variables indicating gene ID, gene number and SNP number within a specific gene respectively. The following 2*Rep (Rep is the number of biological replicates) columns in the data.frame contain count data and the order must be consistent with the sample data. More details would be found in help(mysample).
rep	The number of biological replicates at each SNP.

Value

A data.frame in the structure that would be needed for analysis by BLRM method.

JingXieMIZZOU/BLMRM documentation built on May 29, 2019, 7:31 a.m.