write.fit {limma} | R Documentation

## Write MArrayLM Object to a File

### Description

Write a microarray linear model fit to a file.

### Usage

    write.fit(fit, results = NULL, file, digits = NULL,
              adjust = "none", method = "separate", F.adjust = "none",
              quote = FALSE, sep = "\t", row.names = TRUE, ...)

### Arguments

`fit` | object of class `MArrayLM` containing the results of a linear model fit
`results` | object of class `TestResults`
`file` | character string giving name of file
`digits` | integer indicating rounding precision for output values. If `NULL`, then no rounding is done.
`adjust` | character string specifying multiple-testing adjustment method for the t-statistic P-values, e.g., `"BH"`. See `p.adjust` for the available options. If `NULL` or `"none"` then the P-values are not adjusted.
`method` | character string, should the P-value adjustment be `"global"` or `"separate"` for each contrast.
`F.adjust` | character string specifying adjustment method for the F-statistic P-values.
`quote` | logical. If `TRUE`, any character or factor columns will be surrounded by double quotes.
`sep` | the field separator string. Values in the output file will be separated by this string.
`row.names` | logical, whether to include row names in output file.
`...` | other arguments are passed to `write.table`

### Details

This function writes a tab-delimited text file containing for each gene (1) the average log2-intensity, (2) the coefficients or contrasts (log2-fold-changes), (3) moderated t-statistics, (4) t-statistic P-values, (5) F-statistic if available, (6) F-statistic P-values if available, (7) classification if available and (8) gene names and annotation.

### Value

No value is produced but a file is written to the current working directory.

### Author(s)

Gordon Smyth

### See Also

`write.table` in the base library.

An overview of linear model functions in limma is given by 06.LinearModels.

[Package limma version 3.42.2 Index]