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==Segmentation Programming of PGP1#22== * In /media/Syn_15T/Eric_15T/PGP1_22/BWA samtools view -h s_9_1_Indx49_unique.bam | awk 'BEGIN{FS=OFS="\t"} (/^@/ && !/@SQ/){print $0} $2~/^SN:[1-9]|^SN:X|^SN:Y|^SN:MT/{print $0} $3~/^[1-9]|X|Y|MT/{$3="chr"$3; print $0} ' | sed 's/SN:/SN:chr/g' | sed 's/chrMT/chrM/g' | samtools view -bS - > s_9_1_Indx49_unique.chr.bam samtools index s_9_1_Indx49_unique.chr.bam samtools view -o s_9_1_Indx49_unique.sam s_9_1_Indx49_unique.chr.bam python varbin.50k.sam.py s_9_1_Indx49_unique.sam s_9_1_Indx49.varbin.50k.txt s_9_1_Indx49.varbin.50k.stats.txt samtools view -h s_9_1_Indx50_unique.bam | awk 'BEGIN{FS=OFS="\t"} (/^@/ && !/@SQ/){print $0} $2~/^SN:[1-9]|^SN:X|^SN:Y|^SN:MT/{print $0} $3~/^[1-9]|X|Y|MT/{$3="chr"$3; print $0} ' | sed 's/SN:/SN:chr/g' | sed 's/chrMT/chrM/g' | samtools view -bS - > s_9_1_Indx50_unique.chr.bam samtools index s_9_1_Indx50_unique.chr.bam samtools view -o s_9_1_Indx50_unique.sam s_9_1_Indx50_unique.chr.bam python varbin.50k.sam.py s_9_1_Indx50_unique.sam s_9_1_Indx50.varbin.50k.txt s_9_1_Indx50.varbin.50k.stats.txt samtools view -h s_9_1_Indx51_unique.bam | awk 'BEGIN{FS=OFS="\t"} (/^@/ && !/@SQ/){print $0} $2~/^SN:[1-9]|^SN:X|^SN:Y|^SN:MT/{print $0} $3~/^[1-9]|X|Y|MT/{$3="chr"$3; print $0} ' | sed 's/SN:/SN:chr/g' | sed 's/chrMT/chrM/g' | samtools view -bS - > s_9_1_Indx51_unique.chr.bam samtools index s_9_1_Indx51_unique.chr.bam samtools view -o s_9_1_Indx51_unique.sam s_9_1_Indx51_unique.chr.bam python varbin.50k.sam.py s_9_1_Indx51_unique.sam s_9_1_Indx51.varbin.50k.txt s_9_1_Indx51.varbin.50k.stats.txt samtools view -h s_9_1_Indx52_unique.bam | awk 'BEGIN{FS=OFS="\t"} (/^@/ && !/@SQ/){print $0} $2~/^SN:[1-9]|^SN:X|^SN:Y|^SN:MT/{print $0} $3~/^[1-9]|X|Y|MT/{$3="chr"$3; print $0} ' | sed 's/SN:/SN:chr/g' | sed 's/chrMT/chrM/g' | samtools view -bS - > s_9_1_Indx52_unique.chr.bam samtools index s_9_1_Indx52_unique.chr.bam samtools view -o s_9_1_Indx52_unique.sam s_9_1_Indx52_unique.chr.bam python varbin.50k.sam.py s_9_1_Indx52_unique.sam s_9_1_Indx52.varbin.50k.txt s_9_1_Indx52.varbin.50k.stats.txt samtools view -h s_9_1_Indx53_unique.bam | awk 'BEGIN{FS=OFS="\t"} (/^@/ && !/@SQ/){print $0} $2~/^SN:[1-9]|^SN:X|^SN:Y|^SN:MT/{print $0} $3~/^[1-9]|X|Y|MT/{$3="chr"$3; print $0} ' | sed 's/SN:/SN:chr/g' | sed 's/chrMT/chrM/g' | samtools view -bS - > s_9_1_Indx53_unique.chr.bam samtools index s_9_1_Indx53_unique.chr.bam samtools view -o s_9_1_Indx53_unique.sam s_9_1_Indx53_unique.chr.bam python varbin.50k.sam.py s_9_1_Indx53_unique.sam s_9_1_Indx53.varbin.50k.txt s_9_1_Indx53.varbin.50k.stats.txt samtools view -h s_9_1_Indx54_unique.bam | awk 'BEGIN{FS=OFS="\t"} (/^@/ && !/@SQ/){print $0} $2~/^SN:[1-9]|^SN:X|^SN:Y|^SN:MT/{print $0} $3~/^[1-9]|X|Y|MT/{$3="chr"$3; print $0} ' | sed 's/SN:/SN:chr/g' | sed 's/chrMT/chrM/g' | samtools view -bS - > s_9_1_Indx54_unique.chr.bam samtools index s_9_1_Indx54_unique.chr.bam samtools view -o s_9_1_Indx54_unique.sam s_9_1_Indx54_unique.chr.bam python varbin.50k.sam.py s_9_1_Indx54_unique.sam s_9_1_Indx54.varbin.50k.txt s_9_1_Indx54.varbin.50k.stats.txt samtools view -h s_9_1_Indx55_unique.bam | awk 'BEGIN{FS=OFS="\t"} (/^@/ && !/@SQ/){print $0} $2~/^SN:[1-9]|^SN:X|^SN:Y|^SN:MT/{print $0} $3~/^[1-9]|X|Y|MT/{$3="chr"$3; print $0} ' | sed 's/SN:/SN:chr/g' | sed 's/chrMT/chrM/g' | samtools view -bS - > s_9_1_Indx55_unique.chr.bam samtools index s_9_1_Indx55_unique.chr.bam samtools view -o s_9_1_Indx55_unique.sam s_9_1_Indx55_unique.chr.bam python varbin.50k.sam.py s_9_1_Indx55_unique.sam s_9_1_Indx55.varbin.50k.txt s_9_1_Indx55.varbin.50k.stats.txt samtools view -h s_9_1_Indx56_unique.bam | awk 'BEGIN{FS=OFS="\t"} (/^@/ && !/@SQ/){print $0} $2~/^SN:[1-9]|^SN:X|^SN:Y|^SN:MT/{print $0} $3~/^[1-9]|X|Y|MT/{$3="chr"$3; print $0} ' | sed 's/SN:/SN:chr/g' | sed 's/chrMT/chrM/g' | samtools view -bS - > s_9_1_Indx56_unique.chr.bam samtools index s_9_1_Indx56_unique.chr.bam samtools view -o s_9_1_Indx56_unique.sam s_9_1_Indx56_unique.chr.bam python varbin.50k.sam.py s_9_1_Indx56_unique.sam s_9_1_Indx56.varbin.50k.txt s_9_1_Indx56.varbin.50k.stats.txt samtools view -h s_9_1_Indx57_unique.bam | awk 'BEGIN{FS=OFS="\t"} (/^@/ && !/@SQ/){print $0} $2~/^SN:[1-9]|^SN:X|^SN:Y|^SN:MT/{print $0} $3~/^[1-9]|X|Y|MT/{$3="chr"$3; print $0} ' | sed 's/SN:/SN:chr/g' | sed 's/chrMT/chrM/g' | samtools view -bS - > s_9_1_Indx57_unique.chr.bam samtools index s_9_1_Indx57_unique.chr.bam samtools view -o s_9_1_Indx57_unique.sam s_9_1_Indx57_unique.chr.bam python varbin.50k.sam.py s_9_1_Indx57_unique.sam s_9_1_Indx57.varbin.50k.txt s_9_1_Indx57.varbin.50k.stats.txt samtools view -h s_9_1_Indx58_unique.bam | awk 'BEGIN{FS=OFS="\t"} (/^@/ && !/@SQ/){print $0} $2~/^SN:[1-9]|^SN:X|^SN:Y|^SN:MT/{print $0} $3~/^[1-9]|X|Y|MT/{$3="chr"$3; print $0} ' | sed 's/SN:/SN:chr/g' | sed 's/chrMT/chrM/g' | samtools view -bS - > s_9_1_Indx58_unique.chr.bam samtools index s_9_1_Indx58_unique.chr.bam samtools view -o s_9_1_Indx58_unique.sam s_9_1_Indx58_unique.chr.bam python varbin.50k.sam.py s_9_1_Indx58_unique.sam s_9_1_Indx58.varbin.50k.txt s_9_1_Indx58.varbin.50k.stats.txt samtools view -h s_9_1_Indx59_unique.bam | awk 'BEGIN{FS=OFS="\t"} (/^@/ && !/@SQ/){print $0} $2~/^SN:[1-9]|^SN:X|^SN:Y|^SN:MT/{print $0} $3~/^[1-9]|X|Y|MT/{$3="chr"$3; print $0} ' | sed 's/SN:/SN:chr/g' | sed 's/chrMT/chrM/g' | samtools view -bS - > s_9_1_Indx59_unique.chr.bam samtools index s_9_1_Indx59_unique.chr.bam samtools view -o s_9_1_Indx59_unique.sam s_9_1_Indx59_unique.chr.bam python varbin.50k.sam.py s_9_1_Indx59_unique.sam s_9_1_Indx59.varbin.50k.txt s_9_1_Indx59.varbin.50k.stats.txt samtools view -h s_9_1_Indx60_unique.bam | awk 'BEGIN{FS=OFS="\t"} (/^@/ && !/@SQ/){print $0} $2~/^SN:[1-9]|^SN:X|^SN:Y|^SN:MT/{print $0} $3~/^[1-9]|X|Y|MT/{$3="chr"$3; print $0} ' | sed 's/SN:/SN:chr/g' | sed 's/chrMT/chrM/g' | samtools view -bS - > s_9_1_Indx60_unique.chr.bam samtools index s_9_1_Indx60_unique.chr.bam samtools view -o s_9_1_Indx60_unique.sam s_9_1_Indx60_unique.chr.bam python varbin.50k.sam.py s_9_1_Indx60_unique.sam s_9_1_Indx60.varbin.50k.txt s_9_1_Indx60.varbin.50k.stats.txt samtools view -h s_9_1_Indx61_unique.bam | awk 'BEGIN{FS=OFS="\t"} (/^@/ && !/@SQ/){print $0} $2~/^SN:[1-9]|^SN:X|^SN:Y|^SN:MT/{print $0} $3~/^[1-9]|X|Y|MT/{$3="chr"$3; print $0} ' | sed 's/SN:/SN:chr/g' | sed 's/chrMT/chrM/g' | samtools view -bS - > s_9_1_Indx61_unique.chr.bam samtools index s_9_1_Indx61_unique.chr.bam samtools view -o s_9_1_Indx61_unique.sam s_9_1_Indx61_unique.chr.bam python varbin.50k.sam.py s_9_1_Indx61_unique.sam s_9_1_Indx61.varbin.50k.txt s_9_1_Indx61.varbin.50k.stats.txt samtools view -h s_9_1_Indx62_unique.bam | awk 'BEGIN{FS=OFS="\t"} (/^@/ && !/@SQ/){print $0} $2~/^SN:[1-9]|^SN:X|^SN:Y|^SN:MT/{print $0} $3~/^[1-9]|X|Y|MT/{$3="chr"$3; print $0} ' | sed 's/SN:/SN:chr/g' | sed 's/chrMT/chrM/g' | samtools view -bS - > s_9_1_Indx62_unique.chr.bam samtools index s_9_1_Indx62_unique.chr.bam samtools view -o s_9_1_Indx62_unique.sam s_9_1_Indx62_unique.chr.bam python varbin.50k.sam.py s_9_1_Indx62_unique.sam s_9_1_Indx62.varbin.50k.txt s_9_1_Indx62.varbin.50k.stats.txt samtools view -h s_9_1_Indx63_unique.bam | awk 'BEGIN{FS=OFS="\t"} (/^@/ && !/@SQ/){print $0} $2~/^SN:[1-9]|^SN:X|^SN:Y|^SN:MT/{print $0} $3~/^[1-9]|X|Y|MT/{$3="chr"$3; print $0} ' | sed 's/SN:/SN:chr/g' | sed 's/chrMT/chrM/g' | samtools view -bS - > s_9_1_Indx63_unique.chr.bam samtools index s_9_1_Indx63_unique.chr.bam samtools view -o s_9_1_Indx63_unique.sam s_9_1_Indx63_unique.chr.bam python varbin.50k.sam.py s_9_1_Indx63_unique.sam s_9_1_Indx63.varbin.50k.txt s_9_1_Indx63.varbin.50k.stats.txt samtools view -h s_9_1_Indx64_unique.bam | awk 'BEGIN{FS=OFS="\t"} (/^@/ && !/@SQ/){print $0} $2~/^SN:[1-9]|^SN:X|^SN:Y|^SN:MT/{print $0} $3~/^[1-9]|X|Y|MT/{$3="chr"$3; print $0} ' | sed 's/SN:/SN:chr/g' | sed 's/chrMT/chrM/g' | samtools view -bS - > s_9_1_Indx64_unique.chr.bam samtools index s_9_1_Indx64_unique.chr.bam samtools view -o s_9_1_Indx64_unique.sam s_9_1_Indx64_unique.chr.bam python varbin.50k.sam.py s_9_1_Indx64_unique.sam s_9_1_Indx64.varbin.50k.txt s_9_1_Indx64.varbin.50k.stats.txt samtools view -h s_9_1_Indx65_unique.bam | awk 'BEGIN{FS=OFS="\t"} (/^@/ && !/@SQ/){print $0} $2~/^SN:[1-9]|^SN:X|^SN:Y|^SN:MT/{print $0} $3~/^[1-9]|X|Y|MT/{$3="chr"$3; print $0} ' | sed 's/SN:/SN:chr/g' | sed 's/chrMT/chrM/g' | samtools view -bS - > s_9_1_Indx65_unique.chr.bam samtools index s_9_1_Indx65_unique.chr.bam samtools view -o s_9_1_Indx65_unique.sam s_9_1_Indx65_unique.chr.bam python varbin.50k.sam.py s_9_1_Indx65_unique.sam s_9_1_Indx65.varbin.50k.txt s_9_1_Indx65.varbin.50k.stats.txt samtools view -h s_9_1_Indx66_unique.bam | awk 'BEGIN{FS=OFS="\t"} (/^@/ && !/@SQ/){print $0} $2~/^SN:[1-9]|^SN:X|^SN:Y|^SN:MT/{print $0} $3~/^[1-9]|X|Y|MT/{$3="chr"$3; print $0} ' | sed 's/SN:/SN:chr/g' | sed 's/chrMT/chrM/g' | samtools view -bS - > s_9_1_Indx66_unique.chr.bam samtools index s_9_1_Indx66_unique.chr.bam samtools view -o s_9_1_Indx66_unique.sam s_9_1_Indx66_unique.chr.bam python varbin.50k.sam.py s_9_1_Indx66_unique.sam s_9_1_Indx66.varbin.50k.txt s_9_1_Indx66.varbin.50k.stats.txt samtools view -h s_9_1_Indx67_unique.bam | awk 'BEGIN{FS=OFS="\t"} (/^@/ && !/@SQ/){print $0} $2~/^SN:[1-9]|^SN:X|^SN:Y|^SN:MT/{print $0} $3~/^[1-9]|X|Y|MT/{$3="chr"$3; print $0} ' | sed 's/SN:/SN:chr/g' | sed 's/chrMT/chrM/g' | samtools view -bS - > s_9_1_Indx67_unique.chr.bam samtools index s_9_1_Indx67_unique.chr.bam samtools view -o s_9_1_Indx67_unique.sam s_9_1_Indx67_unique.chr.bam python varbin.50k.sam.py s_9_1_Indx67_unique.sam s_9_1_Indx67.varbin.50k.txt s_9_1_Indx67.varbin.50k.stats.txt samtools view -h s_9_1_Indx68_unique.bam | awk 'BEGIN{FS=OFS="\t"} (/^@/ && !/@SQ/){print $0} $2~/^SN:[1-9]|^SN:X|^SN:Y|^SN:MT/{print $0} $3~/^[1-9]|X|Y|MT/{$3="chr"$3; print $0} ' | sed 's/SN:/SN:chr/g' | sed 's/chrMT/chrM/g' | samtools view -bS - > s_9_1_Indx68_unique.chr.bam samtools index s_9_1_Indx68_unique.chr.bam samtools view -o s_9_1_Indx68_unique.sam s_9_1_Indx68_unique.chr.bam python varbin.50k.sam.py s_9_1_Indx68_unique.sam s_9_1_Indx68.varbin.50k.txt s_9_1_Indx68.varbin.50k.stats.txt samtools view -h s_9_1_Indx69_unique.bam | awk 'BEGIN{FS=OFS="\t"} (/^@/ && !/@SQ/){print $0} $2~/^SN:[1-9]|^SN:X|^SN:Y|^SN:MT/{print $0} $3~/^[1-9]|X|Y|MT/{$3="chr"$3; print $0} ' | sed 's/SN:/SN:chr/g' | sed 's/chrMT/chrM/g' | samtools view -bS - > s_9_1_Indx69_unique.chr.bam samtools index s_9_1_Indx69_unique.chr.bam samtools view -o s_9_1_Indx69_unique.sam s_9_1_Indx69_unique.chr.bam python varbin.50k.sam.py s_9_1_Indx69_unique.sam s_9_1_Indx69.varbin.50k.txt s_9_1_Indx69.varbin.50k.stats.txt samtools view -h s_9_1_Indx70_unique.bam | awk 'BEGIN{FS=OFS="\t"} (/^@/ && !/@SQ/){print $0} $2~/^SN:[1-9]|^SN:X|^SN:Y|^SN:MT/{print $0} $3~/^[1-9]|X|Y|MT/{$3="chr"$3; print $0} ' | sed 's/SN:/SN:chr/g' | sed 's/chrMT/chrM/g' | samtools view -bS - > s_9_1_Indx70_unique.chr.bam samtools index s_9_1_Indx70_unique.chr.bam samtools view -o s_9_1_Indx70_unique.sam s_9_1_Indx70_unique.chr.bam python varbin.50k.sam.py s_9_1_Indx70_unique.sam s_9_1_Indx70.varbin.50k.txt s_9_1_Indx70.varbin.50k.stats.txt samtools view -h s_9_1_Indx71_unique.bam | awk 'BEGIN{FS=OFS="\t"} (/^@/ && !/@SQ/){print $0} $2~/^SN:[1-9]|^SN:X|^SN:Y|^SN:MT/{print $0} $3~/^[1-9]|X|Y|MT/{$3="chr"$3; print $0} ' | sed 's/SN:/SN:chr/g' | sed 's/chrMT/chrM/g' | samtools view -bS - > s_9_1_Indx71_unique.chr.bam samtools index s_9_1_Indx71_unique.chr.bam samtools view -o s_9_1_Indx71_unique.sam s_9_1_Indx71_unique.chr.bam python varbin.50k.sam.py s_9_1_Indx71_unique.sam s_9_1_Indx71.varbin.50k.txt s_9_1_Indx71.varbin.50k.stats.txt samtools view -h s_9_1_Indx72_unique.bam | awk 'BEGIN{FS=OFS="\t"} (/^@/ && !/@SQ/){print $0} $2~/^SN:[1-9]|^SN:X|^SN:Y|^SN:MT/{print $0} $3~/^[1-9]|X|Y|MT/{$3="chr"$3; print $0} ' | sed 's/SN:/SN:chr/g' | sed 's/chrMT/chrM/g' | samtools view -bS - > s_9_1_Indx72_unique.chr.bam samtools index s_9_1_Indx72_unique.chr.bam samtools view -o s_9_1_Indx72_unique.sam s_9_1_Indx72_unique.chr.bam python varbin.50k.sam.py s_9_1_Indx72_unique.sam s_9_1_Indx72.varbin.50k.txt s_9_1_Indx72.varbin.50k.stats.txt perl Segmentation50k_2_state.pl s_9_1_Indx49.varbin.50k.txt PGP1#22_49.csv perl centromereremoval.pl PGP1#22_49.csv PGP1#22Indx49.csv perl Segmentation50k_2_state.pl s_9_1_Indx50.varbin.50k.txt PGP1#22_50.csv perl centromereremoval.pl PGP1#22_50.csv PGP1#22Indx50.csv perl Segmentation50k_2_state.pl s_9_1_Indx51.varbin.50k.txt PGP1#22_51.csv perl centromereremoval.pl PGP1#22_51.csv PGP1#22Indx51.csv perl Segmentation50k_2_state.pl s_9_1_Indx52.varbin.50k.txt PGP1#22_52.csv perl centromereremoval.pl PGP1#22_52.csv PGP1#22Indx52.csv perl Segmentation50k_2_state.pl s_9_1_Indx53.varbin.50k.txt PGP1#22_53.csv perl centromereremoval.pl PGP1#22_53.csv PGP1#22Indx53.csv perl Segmentation50k_2_state.pl s_9_1_Indx54.varbin.50k.txt PGP1#22_54.csv perl centromereremoval.pl PGP1#22_54.csv PGP1#22Indx54.csv perl Segmentation50k_2_state.pl s_9_1_Indx55.varbin.50k.txt PGP1#22_55.csv perl centromereremoval.pl PGP1#22_55.csv PGP1#22Indx55.csv perl Segmentation50k_2_state.pl s_9_1_Indx56.varbin.50k.txt PGP1#22_56.csv perl centromereremoval.pl PGP1#22_56.csv PGP1#22Indx56.csv perl Segmentation50k_2_state.pl s_9_1_Indx57.varbin.50k.txt PGP1#22_57.csv perl centromereremoval.pl PGP1#22_57.csv PGP1#22Indx57.csv perl Segmentation50k_2_state.pl s_9_1_Indx58.varbin.50k.txt PGP1#22_58.csv perl centromereremoval.pl PGP1#22_58.csv PGP1#22Indx58.csv perl Segmentation50k_2_state.pl s_9_1_Indx59.varbin.50k.txt PGP1#22_59.csv perl centromereremoval.pl PGP1#22_59.csv PGP1#22Indx59.csv perl Segmentation50k_2_state.pl s_9_1_Indx60.varbin.50k.txt PGP1#22_60.csv perl centromereremoval.pl PGP1#22_60.csv PGP1#22Indx60.csv perl Segmentation50k_2_state.pl s_9_1_Indx61.varbin.50k.txt PGP1#22_61.csv perl centromereremoval.pl PGP1#22_61.csv PGP1#22Indx61.csv perl Segmentation50k_2_state.pl s_9_1_Indx62.varbin.50k.txt PGP1#22_62.csv perl centromereremoval.pl PGP1#22_62.csv PGP1#22Indx62.csv perl Segmentation50k_2_state.pl s_9_1_Indx62.varbin.50k.txt PGP1#22_63.csv perl centromereremoval.pl PGP1#22_63.csv PGP1#22Indx63.csv perl Segmentation50k_2_state.pl s_9_1_Indx64.varbin.50k.txt PGP1#22_64.csv perl centromereremoval.pl PGP1#22_64.csv PGP1#22Indx64.csv perl Segmentation50k_2_state.pl s_9_1_Indx65.varbin.50k.txt PGP1#22_65.csv perl centromereremoval.pl PGP1#22_65.csv PGP1#22Indx65.csv perl Segmentation50k_2_state.pl s_9_1_Indx66.varbin.50k.txt PGP1#22_66.csv perl centromereremoval.pl PGP1#22_66.csv PGP1#22Indx66.csv perl Segmentation50k_2_state.pl s_9_1_Indx67.varbin.50k.txt PGP1#22_67.csv perl centromereremoval.pl PGP1#22_67.csv PGP1#22Indx67.csv perl Segmentation50k_2_state.pl s_9_1_Indx68.varbin.50k.txt PGP1#22_68.csv perl centromereremoval.pl PGP1#22_68.csv PGP1#22Indx68.csv perl Segmentation50k_2_state.pl s_9_1_Indx69.varbin.50k.txt PGP1#22_69.csv perl centromereremoval.pl PGP1#22_69.csv PGP1#22Indx69.csv perl Segmentation50k_2_state.pl s_9_1_Indx70.varbin.50k.txt PGP1#22_70.csv perl centromereremoval.pl PGP1#22_70.csv PGP1#22Indx70.csv perl Segmentation50k_2_state.pl s_9_1_Indx71.varbin.50k.txt PGP1#22_71.csv perl centromereremoval.pl PGP1#22_71.csv PGP1#22Indx71.csv perl Segmentation50k_2_state.pl s_9_1_Indx72.varbin.50k.txt PGP1#22_72.csv perl centromereremoval.pl PGP1#22_72.csv PGP1#22Indx72.csv y49<-c(scan("PGP1#22Indx49.csv",sep=",")) obj49=smooth.discrete(y49, init=initial, trans=P, parms.emission=B) write.table(t(obj49$s), "obj49.csv", row.names=FALSE, col.names=FALSE, sep=",") y50<-c(scan("PGP1#22Indx50.csv",sep=",")) obj50=smooth.discrete(y50, init=initial, trans=P, parms.emission=B) write.table(t(obj50$s), "obj50.csv", row.names=FALSE, col.names=FALSE, sep=",") y51<-c(scan("PGP1#22Indx51.csv",sep=",")) obj51=smooth.discrete(y51, init=initial, trans=P, parms.emission=B) write.table(t(obj51$s), "obj51.csv", row.names=FALSE, col.names=FALSE, sep=",") y52<-c(scan("PGP1#22Indx52.csv",sep=",")) obj52=smooth.discrete(y52, init=initial, trans=P, parms.emission=B) write.table(t(obj52$s), "obj52.csv", row.names=FALSE, col.names=FALSE, sep=",") y53<-c(scan("PGP1#22Indx53.csv",sep=",")) obj53=smooth.discrete(y53, init=initial, trans=P, parms.emission=B) write.table(t(obj53$s), "obj53.csv", row.names=FALSE, col.names=FALSE, sep=",") y54<-c(scan("PGP1#22Indx54.csv",sep=",")) obj54=smooth.discrete(y54, init=initial, trans=P, parms.emission=B) write.table(t(obj54$s), "obj54.csv", row.names=FALSE, col.names=FALSE, sep=",") y55<-c(scan("PGP1#22Indx55.csv",sep=",")) obj55=smooth.discrete(y55, init=initial, trans=P, parms.emission=B) write.table(t(obj55$s), "obj55.csv", row.names=FALSE, col.names=FALSE, sep=",") y56<-c(scan("PGP1#22Indx56.csv",sep=",")) obj56=smooth.discrete(y56, init=initial, trans=P, parms.emission=B) write.table(t(obj56$s), "obj56.csv", row.names=FALSE, col.names=FALSE, sep=",") y57<-c(scan("PGP1#22Indx57.csv",sep=",")) obj57=smooth.discrete(y57, init=initial, trans=P, parms.emission=B) write.table(t(obj57$s), "obj57.csv", row.names=FALSE, col.names=FALSE, sep=",") y58<-c(scan("PGP1#22Indx58.csv",sep=",")) obj58=smooth.discrete(y58, init=initial, trans=P, parms.emission=B) write.table(t(obj58$s), "obj58.csv", row.names=FALSE, col.names=FALSE, sep=",") y59<-c(scan("PGP1#22Indx59.csv",sep=",")) obj59=smooth.discrete(y59, init=initial, trans=P, parms.emission=B) write.table(t(obj59$s), "obj59.csv", row.names=FALSE, col.names=FALSE, sep=",") y60<-c(scan("PGP1#22Indx60.csv",sep=",")) obj60=smooth.discrete(y60, init=initial, trans=P, parms.emission=B) write.table(t(obj60$s), "obj60.csv", row.names=FALSE, col.names=FALSE, sep=",") y61<-c(scan("PGP1#22Indx61.csv",sep=",")) obj61=smooth.discrete(y61, init=initial, trans=P, parms.emission=B) write.table(t(obj61$s), "obj61.csv", row.names=FALSE, col.names=FALSE, sep=",") y62<-c(scan("PGP1#22Indx62.csv",sep=",")) obj62=smooth.discrete(y62, init=initial, trans=P, parms.emission=B) write.table(t(obj62$s), "obj62.csv", row.names=FALSE, col.names=FALSE, sep=",") y63<-c(scan("PGP1#22Indx63.csv",sep=",")) obj63=smooth.discrete(y63, init=initial, trans=P, parms.emission=B) write.table(t(obj63$s), "obj63.csv", row.names=FALSE, col.names=FALSE, sep=",") y64<-c(scan("PGP1#22Indx64.csv",sep=",")) obj64=smooth.discrete(y64, init=initial, trans=P, parms.emission=B) write.table(t(obj64$s), "obj64.csv", row.names=FALSE, col.names=FALSE, sep=",") y65<-c(scan("PGP1#22Indx65.csv",sep=",")) obj65=smooth.discrete(y65, init=initial, trans=P, parms.emission=B) write.table(t(obj65$s), "obj65.csv", row.names=FALSE, col.names=FALSE, sep=",") y66<-c(scan("PGP1#22Indx66.csv",sep=",")) obj66=smooth.discrete(y66, init=initial, trans=P, parms.emission=B) write.table(t(obj66$s), "obj66.csv", row.names=FALSE, col.names=FALSE, sep=",") y67<-c(scan("PGP1#22Indx67.csv",sep=",")) obj67=smooth.discrete(y67, init=initial, trans=P, parms.emission=B) write.table(t(obj67$s), "obj67.csv", row.names=FALSE, col.names=FALSE, sep=",") y68<-c(scan("PGP1#22Indx68.csv",sep=",")) obj68=smooth.discrete(y68, init=initial, trans=P, parms.emission=B) write.table(t(obj68$s), "obj68.csv", row.names=FALSE, col.names=FALSE, sep=",") y69<-c(scan("PGP1#22Indx69.csv",sep=",")) obj69=smooth.discrete(y69, init=initial, trans=P, parms.emission=B) write.table(t(obj69$s), "obj69.csv", row.names=FALSE, col.names=FALSE, sep=",") y70<-c(scan("PGP1#22Indx70.csv",sep=",")) obj70=smooth.discrete(y70, init=initial, trans=P, parms.emission=B) write.table(t(obj70$s), "obj70.csv", row.names=FALSE, col.names=FALSE, sep=",") y71<-c(scan("PGP1#22Indx71.csv",sep=",")) obj71=smooth.discrete(y71, init=initial, trans=P, parms.emission=B) write.table(t(obj71$s), "obj71.csv", row.names=FALSE, col.names=FALSE, sep=",") y72<-c(scan("PGP1#22Indx72.csv",sep=",")) obj72=smooth.discrete(y72, init=initial, trans=P, parms.emission=B) write.table(t(obj72$s), "obj72.csv", row.names=FALSE, col.names=FALSE, sep=",") perl SegmentationStatBatch.pl perl global2chromosomePos.pl obj49.csv.pos PGP1_22_FragmentBoundaryCh1.bed perl global2chromosomePos.pl obj50.csv.pos PGP1_22_FragmentBoundaryCh2.bed perl global2chromosomePos.pl obj51.csv.pos PGP1_22_FragmentBoundaryCh3.bed perl global2chromosomePos.pl obj52.csv.pos PGP1_22_FragmentBoundaryCh4.bed perl global2chromosomePos.pl obj53.csv.pos PGP1_22_FragmentBoundaryCh5.bed perl global2chromosomePos.pl obj54.csv.pos PGP1_22_FragmentBoundaryCh6.bed perl global2chromosomePos.pl obj55.csv.pos PGP1_22_FragmentBoundaryCh7.bed perl global2chromosomePos.pl obj56.csv.pos PGP1_22_FragmentBoundaryCh8.bed perl global2chromosomePos.pl obj57.csv.pos PGP1_22_FragmentBoundaryCh9.bed perl global2chromosomePos.pl obj58.csv.pos PGP1_22_FragmentBoundaryCh10.bed perl global2chromosomePos.pl obj59.csv.pos PGP1_22_FragmentBoundaryCh11.bed perl global2chromosomePos.pl obj60.csv.pos PGP1_22_FragmentBoundaryCh12.bed perl global2chromosomePos.pl obj61.csv.pos PGP1_22_FragmentBoundaryCh13.bed perl global2chromosomePos.pl obj62.csv.pos PGP1_22_FragmentBoundaryCh14.bed perl global2chromosomePos.pl obj63.csv.pos PGP1_22_FragmentBoundaryCh15.bed perl global2chromosomePos.pl obj64.csv.pos PGP1_22_FragmentBoundaryCh16.bed perl global2chromosomePos.pl obj65.csv.pos PGP1_22_FragmentBoundaryCh17.bed perl global2chromosomePos.pl obj66.csv.pos PGP1_22_FragmentBoundaryCh18.bed perl global2chromosomePos.pl obj67.csv.pos PGP1_22_FragmentBoundaryCh19.bed perl global2chromosomePos.pl obj68.csv.pos PGP1_22_FragmentBoundaryCh20.bed perl global2chromosomePos.pl obj69.csv.pos PGP1_22_FragmentBoundaryCh21.bed perl global2chromosomePos.pl obj70.csv.pos PGP1_22_FragmentBoundaryCh22.bed perl global2chromosomePos.pl obj71.csv.pos PGP1_22_FragmentBoundaryCh23.bed perl global2chromosomePos.pl obj72.csv.pos PGP1_22_FragmentBoundaryCh24.bed
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