| Title: | A suite of functions to facilitate zFPKM transformations |
|---|---|
| Description: | Perform the zFPKM transform on RNA-seq FPKM data. This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID 24215113). Reference recommends using zFPKM > -3 to select expressed genes. Validated with encode open/closed chromosome data. Works well for gene level data using FPKM or TPM. Does not appear to calibrate well for transcript level data. |
| Authors: | Ron Ammar [aut, cre], John Thompson [aut] |
| Maintainer: | Ron Ammar <[email protected]> |
| License: | GPL-3 | file LICENSE |
| Version: | 1.29.0 |
| Built: | 2024-11-18 04:56:02 UTC |
| Source: | https://github.com/bioc/zFPKM |
Perform the zFPKM transform on RNA-seq FPKM data. This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID 24215113). Reference recommends using zFPKM > -3 to select expressed genes. Validated with encode open/closed promoter chromatin structure epigenetic data on six of the ENCODE cell lines. Works well for gene level data using FPKM or TPM. Does not appear to calibrate well for transcript level data.
zFPKM(fpkmDF, assayName = "fpkm")zFPKM(fpkmDF, assayName = "fpkm")
fpkmDF |
A SummarizedExperiment or data frame containing raw FPKM (or TPM) values. Each row corresponds to a gene/transcript and each column corresponds to a sample. NOTE: these are NOT log_2 transformed. Also, the rownames are gene/transcript names and NOT included as a separate column |
assayName |
When input is a SummarizedExperiment, names the specific assay. Typically one of "fpkm" or "tpm" [default = "fpkm"] |
zFPKM data frame
Ron Ammar, [email protected]
http://www.ncbi.nlm.nih.gov/pubmed/24215113
library(dplyr) gse94802 <- "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94802/suppl/GSE94802_Minkina_etal_normalized_FPKM.csv.gz" temp <- tempfile() download.file(gse94802, temp) fpkm <- read.csv(gzfile(temp), row.names=1) MyFPKMdf <- select(fpkm, -MGI_Symbol) zfpkm <- zFPKM(MyFPKMdf)library(dplyr) gse94802 <- "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94802/suppl/GSE94802_Minkina_etal_normalized_FPKM.csv.gz" temp <- tempfile() download.file(gse94802, temp) fpkm <- read.csv(gzfile(temp), row.names=1) MyFPKMdf <- select(fpkm, -MGI_Symbol) zfpkm <- zFPKM(MyFPKMdf)
Perform the zFPKM transform on RNA-seq FPKM data. This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID 24215113). Reference recommends using zFPKM > -3 to select expressed genes. Validated with encode open/closed promoter chromatin structure epigenetic data on six of the ENCODE cell lines. Works well for gene level data using FPKM or TPM. Does not appear to calibrate well for transcript level data.
zFPKMPlot(fpkmDF, assayName = "fpkm", FacetTitles = FALSE, PlotXfloor = -20)zFPKMPlot(fpkmDF, assayName = "fpkm", FacetTitles = FALSE, PlotXfloor = -20)
fpkmDF |
A SummarizedExperiment or data frame containing raw FPKM (or TPM) values. Each row corresponds to a gene/transcript and each column corresponds to a sample. NOTE: these are NOT log_2 transformed. Also, the rownames are gene/transcript names and NOT included as a separate column |
assayName |
When input is a SummarizedExperiment, names the specific assay. Typically one of "fpkm" or "tpm" [default = "fpkm"] |
FacetTitles |
use to label each facet with the sample name [default = FALSE] |
PlotXfloor |
Lower limit for X axis (log2FPKM units) [default = -20] set to NULL to disable |
Displays plots of zFPKM distributions
Ron Ammar, [email protected]
http://www.ncbi.nlm.nih.gov/pubmed/24215113
library(dplyr) gse94802 <- "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94802/suppl/GSE94802_Minkina_etal_normalized_FPKM.csv.gz" temp <- tempfile() download.file(gse94802, temp) fpkm <- read.csv(gzfile(temp), row.names=1) MyFPKMdf <- select(fpkm, -MGI_Symbol) zFPKMPlot(MyFPKMdf)library(dplyr) gse94802 <- "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94802/suppl/GSE94802_Minkina_etal_normalized_FPKM.csv.gz" temp <- tempfile() download.file(gse94802, temp) fpkm <- read.csv(gzfile(temp), row.names=1) MyFPKMdf <- select(fpkm, -MGI_Symbol) zFPKMPlot(MyFPKMdf)