tx_generatePairedEndFASTQ | R Documentation |
Simulates a paired-end FASTQ files from a genome and a gene annotation. The distribution of reads is randomly selected following a negative binomial distribution.
tx_generatePairedEndFASTQ(
genome,
geneAnnot,
readLen_1,
readLen_2,
insertSize,
libSize,
fileName_r1,
fileName_r2,
TPM = NULL,
NB_r = 5,
NB_mu = 500,
nCores
)
genome |
list. The full reference genome sequences, as loaded by
|
geneAnnot |
GRanges. Gene annotation as loaded by |
readLen_1 |
integer. Length of simulated reads1 |
readLen_2 |
integer. Length of simulated reads2 |
insertSize |
integer. Length of simulated insert (gap between reads) |
libSize |
integer. Size of simulated FASTQ file |
fileName_r1 |
character. Name of output file reads1. |
fileName_r2 |
character. Name of output file reads2. |
TPM |
numeric. Proportion of reads per gene in gene annotation. Overrides negative binomial distribution generation. |
NB_r |
numeric. Target r dispersion parameter. Bigger values of r tend to generate a normal distribution. See ?stats::rnbinom() |
NB_mu |
numeric. Target mean of the resulting distribution |
nCores |
integer. Number of cores to run the function with. Multicore capability not available in Windows OS. |
Writes FASTQ files fileName_r1 and fileName_r2
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