Description Usage Arguments Examples
Run differential expression analysis
1 2 3 4 5 |
sample.info |
character string giving the path to a tab-delimited text file with at least the columns <condition> (treatment condition), <sample> (sample name), and <file1> (absolute or relative path to the fastq or salmon quant.sf files). If fastq files and PE reads, then a column <file2> should also be present. If a batch effect is to be included in the design, then this should be identified under the column <batch>. |
reference |
character vector specifying the conditions in order. For example,
c("A", "B", "C", "D") would mean "A" is the reference condition to which "B", "C"
and "D" are compared; in addition, "C" and "D" will be compared to "B", and "D"
will be compared to "C". If |
species |
character string specifying the name of the species. Only
|
output.dir |
character string specifying the directory to which results will be saved. If the directory does not exist, it will be created. |
threads |
an integer value indicating the number of parallel threads to be used by FastQC. [DEFAULT = maximum number of available threads - 1]. |
fastqc |
a character string specifying the path to the fastqc executable. [DEFAULT = "fastqc"]. |
multiqc |
a character string specifying the path to the multiqc executable. [DEFAULT = "multiqc"]. |
index.dir |
directory of the index files needed for read mapping using Salmon.
See function |
salmon |
a character string specifying the path to the salmon executable. [DEFAULT = "salmon"]. |
bam |
logical, if |
bootstraps |
integer giving the number of bootstrap samples that Salmon should use (default is 0). With bootstrap samples, uncertainty in abundance can be quantified. |
seqBias |
logical, should Salmon's option be used to model and correct
abundances for sequence specific bias? Default is |
gcBias |
logical, should Salmon's option be used to model and correct
abundances for GC content bias? Requires Salmon version 0.7.2 or higher.
Default is |
posBias |
logical, should Salmon's option be used to model and correct
abundances for positional biases? Requires Salmon version 0.7.3 or higher.
Default is |
allowOrphans |
logical, if |
advanced.opts |
character vector supplying list of advanced option
arguments to apply to each Salmon call. For details see Salmon documentation
or type |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | ## Not run:
targets.file <- data.frame(
file1 = list.files(system.file("extdata/FASTQ/", package = "rseqR"),
"*_1.fastq", full.names = TRUE),
file2 = list.files(system.file("extdata/FASTQ/", package = "rseqR"),
"*_2.fastq", full.names = TRUE),
sample = c("BUFF1", "BUFF2", "OX1", "OX2", "UNT1", "UNT2"),
condition = c(rep("BUFF", 2), rep("OX", 2), rep("UNT", 2)),
batch = rep(1:2, times = 3))
write.table(targets.file, "targets.txt", col.names = TRUE,
row.names = FALSE, sep = "\t", quote = FALSE)
run_dea(sample.info = "targets.txt", reference = c("UNT", "BUFF", "OX"),
species = "human", output.dir = "results", index.dir = NULL)
## End(Not run)
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