getSGFeatureCounts: Compatible counts for splice graph features from BAM files
In SGSeq: Splice event prediction and quantification from RNA-seq data

Compatible counts are obtained for each sample and combined into an SGFeatureCounts object.

1 2	getSGFeatureCounts(sample_info, features, min_anchor = 1, counts_only = FALSE, verbose = FALSE, cores = 1)

`sample_info`	Data frame with sample information. Required columns are “sample_name”, “file_bam”, “paired_end”, “read_length”, “frag_length” and “lib_size”. Library information can be obtained with function `getBamInfo`.
`features`	`SGFeatures` object
`min_anchor`	Integer specifiying minimum anchor length
`counts_only`	Logical indicating only counts should be returned
`verbose`	If `TRUE`, generate messages indicating progress
`cores`	Number of cores available for parallel processing

codeSGFeatureCounts object, or integer matrix of counts if counts_only = TRUE

Leonard Goldstein

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path <- system.file("extdata", package = "SGSeq")
si$file_bam <- file.path(path, "bams", si$file_bam)
sgfc <- getSGFeatureCounts(si, sgf_pred)

SGSeq documentation built on Nov. 8, 2020, 8:31 p.m.

SGSeq index

Splice event prediction and quantification from RNA-seq data

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