1. rcellminer
  2. man
  3. getBinaryMutationData.Rd
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Added importFrom statements Edited vignette to remove structure related sections Remove structure related tests Updated Rd files

cannin authored on 17/04/2020 15:48:36
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man/getBinaryMutationData.Rd
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@@ -5,9 +5,14 @@
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 \title{Compute a binary gene mutation data matrix from SNP and other mutation
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 event-level data.}
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 \usage{
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-getBinaryMutationData(mutInfo, mutData, maxVariantFreq = 0.2,
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-  maxNormalPopulationFreq = 0.005, maxSiftScore = 0.05,
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-  minPolyPhenScore = 0.85)
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+getBinaryMutationData(
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+  mutInfo,
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+  mutData,
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+  maxVariantFreq = 0.2,
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+  maxNormalPopulationFreq = 0.005,
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+  maxSiftScore = 0.05,
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+  minPolyPhenScore = 0.85
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+)
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 }
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 \arguments{
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 \item{mutInfo}{A data frame with the following named columns:
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@@ -48,6 +53,4 @@ along columns, and 1s indicating deleterious mutations.
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 Compute a binary gene mutation data matrix from SNP and other mutation
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 event-level data.
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 }
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-\concept{
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-rcellminer
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-}
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+\concept{rcellminer}
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Minor documentation update Updated analytics Updated about.md

cannin authored on 29/03/2017 21:43:19
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man/getBinaryMutationData.Rd
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@@ -51,4 +51,3 @@ event-level data.
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 \concept{
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 rcellminer
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 }
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-
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Adding parCorPatternComparison() function to do pattern comparisons based on partial correlations with respect to a fixed pattern (whose influence with respect to a linear model is to be excluded).

Vinodh N. Rajapakse authored on 09/08/2016 18:28:29
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man/getBinaryMutationData.Rd
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@@ -1,4 +1,4 @@
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-% Generated by roxygen2 (4.1.1): do not edit by hand
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+% Generated by roxygen2: do not edit by hand
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 % Please edit documentation in R/getBinaryMutationData.R
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 \name{getBinaryMutationData}
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 \alias{getBinaryMutationData}
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@@ -15,7 +15,7 @@ Gene, the name of the gene associated with the mutation event;
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 probe.ids, a unique identifier specifying the mutation event;
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 SNP_1000_genome, the frequency of the mutation event in SNP 1000;
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 ESP5400, the frequency of the mutation event in ESP5400;
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-SNP_type, the type of mutation event, chosen from "MISSENSE", "FRAMESHIFT",
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+SNP_type, the type of mutation event, chosen from "MISSENSE", "FRAMESHIFT",
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 "NONFRAMESHIFT", "NONSENSE", "SPLICING";
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 SIFT_score, the SIFT score;
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 Polyphen_score, the POLYPHEN score.
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@@ -34,7 +34,7 @@ exclude frequently occuring events); default value = 0.2.}
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 \item{maxNormalPopulationFreq}{The maximum freqency of a mutation in the normal
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 population (used to exclude likely germline variants); default value = 0.005.}
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-\item{maxSiftScore}{The maximum accepted SIFT score (used to exclude
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+\item{maxSiftScore}{The maximum accepted SIFT score (used to exclude
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 presumed non-deleterious mutations); default value = 0.05.}
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 \item{minPolyPhenScore}{The minimum accepted POLYPHEN score (used to
Browse code

Initial commit

cannin authored on 25/02/2016 02:26:31
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man/getBinaryMutationData.Rd
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new file mode 100644
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+% Generated by roxygen2 (4.1.1): do not edit by hand
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+% Please edit documentation in R/getBinaryMutationData.R
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+\name{getBinaryMutationData}
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+\alias{getBinaryMutationData}
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+\title{Compute a binary gene mutation data matrix from SNP and other mutation
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+event-level data.}
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+\usage{
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+getBinaryMutationData(mutInfo, mutData, maxVariantFreq = 0.2,
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+  maxNormalPopulationFreq = 0.005, maxSiftScore = 0.05,
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+  minPolyPhenScore = 0.85)
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+}
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+\arguments{
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+\item{mutInfo}{A data frame with the following named columns:
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+Gene, the name of the gene associated with the mutation event;
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+probe.ids, a unique identifier specifying the mutation event;
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+SNP_1000_genome, the frequency of the mutation event in SNP 1000;
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+ESP5400, the frequency of the mutation event in ESP5400;
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+SNP_type, the type of mutation event, chosen from "MISSENSE", "FRAMESHIFT",
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+"NONFRAMESHIFT", "NONSENSE", "SPLICING";
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+SIFT_score, the SIFT score;
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+Polyphen_score, the POLYPHEN score.
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+Rownames of mutInfo should be set to probe.ids, i.e., the unique mutation
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+event specifier.}
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+
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+\item{mutData}{A matrix with event level mutation information, with SNPs, etc.
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+along rows and samples along columns.  Rownames of mutData should exactly
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+match those of mutInfo.  The i-th row of mutInfo should thus give detailed
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+information for the mutation event with data specified in the i-th row of
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+mutData.}
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+
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+\item{maxVariantFreq}{The maximum proportion of mutant samples (used to
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+exclude frequently occuring events); default value = 0.2.}
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+
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+\item{maxNormalPopulationFreq}{The maximum freqency of a mutation in the normal
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+population (used to exclude likely germline variants); default value = 0.005.}
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+
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+\item{maxSiftScore}{The maximum accepted SIFT score (used to exclude
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+presumed non-deleterious mutations); default value = 0.05.}
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+
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+\item{minPolyPhenScore}{The minimum accepted POLYPHEN score (used to
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+exclude presumed non-deleterious mutations); default value = 0.85.}
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+}
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+\value{
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+A binary gene mutation matrix, with genes along rows, samples
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+along columns, and 1s indicating deleterious mutations.
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+}
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+\description{
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+Compute a binary gene mutation data matrix from SNP and other mutation
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+event-level data.
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+}
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+\concept{
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+rcellminer
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+}
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+