Description Usage Arguments Details Value Author(s) References See Also Examples
View source: R/getLimmaInput.DF.R
Fits the linear model log2(count+scalefac) = beta0 +
beta1*group + beta2*library.size + [optional confounders]
to each nucleotide. From these models, this function
constructs an object which can be directly passed to
getTstats
to obtain limma
's moderated t
statistics for each nucleotide, which we use as a measure
of strength of association between group and count
(expression). Reads coverage from a DataFrame which can be
generated using makeDF
and relies heavily on the
limma
package, using lmFit
as the main
workhorse.
1 2 3 |
DF |
A list containing a |
comparison |
Either |
group |
a 0/1 vector grouping the samples (columns) in the database. |
chunksize |
How many rows of the merged table should be processed at a time? |
adjustvars |
Optional matrix of adjustment variables (e.g. measured confounders, output from SVA, etc.) to use in fitting linear models to each nucleotide. |
colsubset |
Optional vector of column indices of the input file that denote samples you wish to include in analysis. |
scalefac |
A log transformation is used on the count tables, so zero counts present a problem. What number should we add to the entire matrix before running the models? Defaults to 32. |
nonzero |
If TRUE, use the median of only the nonzero counts as the library size adjustment. |
Note adjustvars
must have the same number of rows as
group
has entries. Larger values of chunksize
require more memory; smaller values of chunksize
require more computation time.
A list with elements
ebobject |
A list of five
vectors ( |
pos |
A vector of the same length as those contained
in |
Alyssa Frazee, Leonardo Collado-Torres
Smyth G (2004). "Linear models and empirical Bayes methods for assessing differential expression in microarray experiments." Statistical Applications in Genetics and Molecular Biology 3(1): Article 3.
1 | ## add example here when we have a vignette
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.