SetATGas0: Set Position of ATG as Zero

Description

Set position of ATG as zero in hap result and gff annotation. The upstream was negative while the gene range and downstream was positive.

Usage

gffSetATGas0(gff = gff, hap = hap,
             geneID = geneID,
             Chr = Chr, POS = POS)
hapSetATGas0(gff = gff, hap = hap,
             geneID = geneID,
             Chr = Chr, POS = POS)

Value

gffSetATGas0: filtered gff with position of ATG was as zero

hapSetATGas0: hap results with position of ATG was set as zero

Arguments

gff: gene annotations
hap: object of hapResult or hapSummary class
geneID: geneID
Chr: Chromsome name
POS: vector consist with start and end position

Details

Filter hap result and gff annotation according to provided information. And then set position of ATG as zero in hap result and gff annotation. The upstream was negative while the gene range and downstream was positive.

Notice: the position of "ATG" after modified was 0, 1 and 2 separately. The site in hap result exceed the selected range will be dropped.

Examples

Run this code

# \donttest{
# load example dataset
data("geneHapR_test")


# set position of ATG as zero in gff
newgff <- gffSetATGas0(gff = gff, hap = hapResult,
                       geneID = "test1G0387",
                       Chr = "scaffold_1",
                       POS = c(4300, 7910))

# }
data("geneHapR_test")

# set position of ATG as zero in hap results
newhapResult <- hapSetATGas0(gff = gff, hap = hapResult,
                             geneID = "test1G0387",
                             Chr = "scaffold_1",
                             POS = c(4300, 7910))