writefit: Write MArrayLM Object to a File

Description Usage Arguments Details Value Author(s) See Also Examples

Description

Write a microarray linear model fit to a file.

Usage

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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

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## 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)

hdeberg/limma documentation built on Dec. 20, 2021, 3:43 p.m.