compareSampleGroups: compareSampleGroups

In adamstruck/RECD: Repeat Exansion & Contraction Detection

Description

Perform a Student's t-test or a Spearmans's correlation test on different groups of your data.

Usage

  compareSampleGroups(merged_sample_data, pheno_table,
    grouping = list(list(name = "plot.metaclass")),
    test = "ttest", matched_patient_tissues = FALSE,
    output_file)

Arguments

merged_sample_data	A data frame of numerical data that you wish to group and compare using a student's t-test.
pheno_table	A data frame giving the group labels (phenotypic data) for each point in ‘merged_sample_data’. It should have the same number of rows as ‘merged_sample_data’ is long. If ‘merged_sample_data’ is named and ‘pdata’ has rownames then they are checked for equality.
grouping	A list specifying the levels of grouping your data based on the ‘pdata’. Each entry of the list has several componenets: $name The name of a field from ‘pdata’ $level a specific level of the specified $name to filter the data by. Only samples with this level will be considered. ONLY ONE $NAME CAN BE SPECIFIED WITHOUT A CORRESPONDING LEVEL.
test	"ttest" or "cor"; perform either a student's t test on the supplied data or calculate the Spearmans' correlation between patient tumor/normal samples.
matched_patient_tissues	logical, if TRUE only samples with matched tumor and normal samples will be considered.
output_file	Desired name of output file

Details

See below:

Value

TSV file containing t-test statistics for each repeat

Author(s)

Adam Struck - Intern

adamstruck/RECD documentation built on May 10, 2019, 5:51 a.m.