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 path name for the output 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. Ignored if `adjust = "none"`.
`F.adjust` | character string specifying adjustment method for the F-statistic P-values.
`quote` | logical value. 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 value, whether to include row names in the output file.
`...` | other arguments are passed to `write.table`.

### Details

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

The `results` argument is optional. If supplied, it should be the output from `decideTests` for the same fit object, which indicates whether each contrast for each gene is considered statistically significant or not (coded 1 or -1 for positive or negative significant differences and 0 for non-significant values).

If `fit` contains row names and `row.names=TRUE`, then the row names will be the first column of the output file with a blank column heading. This behaviour is analogous to that of `write.csv` or to `write.table` with `col.names=NA`.

### Value

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

### Author(s)

Gordon Smyth

### See Also

`write.table` or `write.csv` in the base library.

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

### Examples

    ## Not run:
    # The following three alternatives are equivalent:
    write.fit(fit, file = "temp.csv", sep = ",")
    write.csv(fit, file = "temp.csv")
    a <- as.data.frame(fit)
    write.csv(fit, file = "temp.csv")

    ## End(Not run)

[Package limma version 3.50.3 Index]