| do not use the username\document\somethingpath | |
| use the below path | |
| .libPaths(.libPaths()[2]) |
| z.test <- function(x,n,p=NULL,conf.level=0.95,alternative="less") { | |
| ts.z <- NULL | |
| cint <- NULL | |
| p.val <- NULL | |
| phat <- x/n | |
| qhat <- 1 - phat | |
| # If you have p0 from the population or H0, use it. | |
| # Otherwise, use phat and qhat to find SE.phat: | |
| if(length(p) > 0) { | |
| q <- 1-p |
| birth <- function(n) { | |
| deno <- 365^n | |
| nume <- prod(365:(365-n+1)) | |
| result <- 1- (nume / deno) | |
| return(result) | |
| } | |
| nrep <- 10000 |
| Sys.setlocale("LC_ALL", "korean") | |
| 요인 | 제곱합 | 자유도 | 평균제곱 | F비 |
|---|---|---|---|---|
| 회귀 | SSR | MSR=SSR/1 | F0=MSR/MSE | |
| 오차 | SSE | MSE=SSE/(n-2) | ||
| 전체 | SST |
SSR = sigma (yhat.i - ymean)**2 = Regression of Sum of Squares
SSE = sigma (y.i - yhat.i) ** 2 = Error of Sum of Squares
SST = sigma (y.i - ymean)**2 = Toatal Sum of Squares
| order matters | order doesn't matter | |
|---|---|---|
| replacement | n^^k | (n+k-1 choose k) |
| don't replace | n(n-1)/(n-k+1) | (n choose k) |
| cat SRR_Acc_List.txt | xargs -I {} fastq-dump -split-3 --gzip {} |
| Line=0 | |
| for var in "$@" | |
| do | |
| Line=`grep -c ">" $var` | |
| echo $var $Line >> read.cnt.log | |
| done | |
| cat read.cnt.log | sort -k 2 -r |
| Line=0 | |
| for var in "$@" | |
| do | |
| Line=`zcat $var | wc -l` | |
| echo $var $((Line/4)) >> read.cnt.log | |
| done | |
| cat read.cnt.log | sort -k 2 -r |
| STAR_INDEX="/home/mRNAseq/ref/gencode/human/GRCh37.19/idx/" | |
| INPUT_DIR="00_raw_fastq" | |
| OUTPUT_DIR="01_alignment_genes_count" | |
| GTF="/home/mRNAseq/ref/gencode/human/GRCh37.19/gtf/gencode.v19.annotation.gtf" | |
| RSEM_INDEX="/home/mRNAseq/ref/gencode/human/GRCh37.19/idx/GRCh37.p13.genome" | |
| mkdir -p $OUTPUT_DIR | |
| cat samples.list | parallel --jobs 1 "mkdir -p $OUTPUT_DIR/{}" |